From 2cadb018c56b2dc6a8bf334693db6a31f3e557a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Tue, 9 Jul 2024 11:24:59 +0200 Subject: [PATCH 01/61] Update ubuntu and actions checkout versions --- .github/workflows/build.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 06452bd45..7cbb70d41 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -14,13 +14,13 @@ name: Build jobs: build_and_test: - runs-on: ubuntu-20.04 + runs-on: ubuntu-22.04 strategy: matrix: - arch: [x86_64, aarch64] + arch: [x86_64] #aarch64 steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Build trimal for Linux x86_64 if: matrix.arch == 'x86_64' run: cd source && make all && file trimal && file readal && file statal && @@ -31,7 +31,7 @@ jobs: uses: uraimo/run-on-arch-action@v2 with: arch: ${{ matrix.arch }} - distro: ubuntu20.04 + distro: ubuntu22.04 githubToken: ${{ github.token }} dockerRunArgs: | --volume "${PWD}:/trimal" From b84b935620e4bc028eacd7e1d942b2b487fd299d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Tue, 9 Jul 2024 11:27:06 +0200 Subject: [PATCH 02/61] Add file to force workflow run --- scripts/dummy-file.txt | 1 + 1 file changed, 1 insertion(+) create mode 100644 scripts/dummy-file.txt diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt new file mode 100644 index 000000000..30096e3de --- /dev/null +++ b/scripts/dummy-file.txt @@ -0,0 +1 @@ +Temporary file to force Github Actions workflow to be launched From e0647f3787df2306bb64e4bd1d0307dad14e45ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Tue, 9 Jul 2024 15:29:18 +0200 Subject: [PATCH 03/61] Add first Windows build and test --- .github/workflows/build.yml | 26 +++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 7cbb70d41..40ed32ba3 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -13,7 +13,7 @@ on: name: Build jobs: - build_and_test: + build_and_test_linux: runs-on: ubuntu-22.04 strategy: matrix: @@ -41,3 +41,27 @@ jobs: run: | cd /trimal/source && make all && file trimal && file readal && file statal && cd .. && ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh + build_and_test_windows: + runs-on: windows-2022 + steps: + #- uses: actions/checkout@v4 + - name: Download Release Binaries + run: | + curl -L -o trimal.zip https://github.com/inab/trimal/releases/download/v1.5.0/trimAl_Windows_x86-64.zip + + - name: Unzip Binaries + run: | + powershell -Command "Expand-Archive -Path trimal.zip -DestinationPath ." + + - name: Verify Binaries + run: | + # Use PowerShell or native Windows commands to verify binaries + Get-Command .\trimAl_Windows_x86-64\trimal.exe + Get-Command .\trimAl_Windows_x86-64\readal.exe + Get-Command .\trimAl_Windows_x86-64\statal.exe + + - name: Run Tests on Binaries + run: | + .\trimAl_Windows_x86-64\trimal.exe --help + .\trimAl_Windows_x86-64\readal.exe --help + .\trimAl_Windows_x86-64\statal.exe --help From c068757c078aed404f205c39ca81e52c892289e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Tue, 9 Jul 2024 15:29:57 +0200 Subject: [PATCH 04/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 30096e3de..1f9a8f15a 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched +Temporary file to force Github Actions workflow to be launched. From 1bd5b923da7c60e3139ae276440276550a9ff5d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:09:46 +0200 Subject: [PATCH 05/61] Debug Windows workflow error --- .github/workflows/build.yml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 40ed32ba3..5f2af1efd 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -61,7 +61,12 @@ jobs: Get-Command .\trimAl_Windows_x86-64\statal.exe - name: Run Tests on Binaries + continue-on-error: true run: | - .\trimAl_Windows_x86-64\trimal.exe --help - .\trimAl_Windows_x86-64\readal.exe --help - .\trimAl_Windows_x86-64\statal.exe --help + .\trimAl_Windows_x86-64\trimal.exe --help 2>&1 | tee trimal_help.txt + + - name: Display Logs + if: failure() + run: | + echo trimal.exe --help output: + type trimal_help.txt From 155fb3046f0af83cee50d81bb7207912b8d45beb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:10:10 +0200 Subject: [PATCH 06/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 1f9a8f15a..30096e3de 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched. +Temporary file to force Github Actions workflow to be launched From eb611f885bdef383eee68762a38503d7437ee784 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:13:39 +0200 Subject: [PATCH 07/61] Debug Windows binaries dependencies --- .github/workflows/build.yml | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 5f2af1efd..d7231e94d 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -52,14 +52,21 @@ jobs: - name: Unzip Binaries run: | powershell -Command "Expand-Archive -Path trimal.zip -DestinationPath ." - + - name: List Directory Contents + run: | + dir .\trimAl_Windows_x86-64\ + - name: Verify Binaries run: | # Use PowerShell or native Windows commands to verify binaries Get-Command .\trimAl_Windows_x86-64\trimal.exe Get-Command .\trimAl_Windows_x86-64\readal.exe Get-Command .\trimAl_Windows_x86-64\statal.exe - + + - name: Check Binary Dependencies + run: | + "C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.28.29910\bin\Hostx64\x64\dumpbin.exe" /DEPENDENTS .\trimAl_Windows_x86-64\trimal.exe + - name: Run Tests on Binaries continue-on-error: true run: | From 2e443ccd13a9e98c42d214fb2052869ea0c1c203 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:13:59 +0200 Subject: [PATCH 08/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 30096e3de..1f9a8f15a 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched +Temporary file to force Github Actions workflow to be launched. From 0e1ee46453b06cdb53a1df56de5831ac27d953fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:23:12 +0200 Subject: [PATCH 09/61] Run workflow only on new Windows binaries --- .github/workflows/build.yml | 41 +------------------------------------ 1 file changed, 1 insertion(+), 40 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index d7231e94d..43c38461f 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -13,34 +13,6 @@ on: name: Build jobs: - build_and_test_linux: - runs-on: ubuntu-22.04 - strategy: - matrix: - arch: [x86_64] #aarch64 - - steps: - - uses: actions/checkout@v4 - - name: Build trimal for Linux x86_64 - if: matrix.arch == 'x86_64' - run: cd source && make all && file trimal && file readal && file statal && - cd .. && ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh - - - name: Build trimal for Linux aarch64 - if: matrix.arch == 'aarch64' - uses: uraimo/run-on-arch-action@v2 - with: - arch: ${{ matrix.arch }} - distro: ubuntu22.04 - githubToken: ${{ github.token }} - dockerRunArgs: | - --volume "${PWD}:/trimal" - install: | - apt-get update -q -y - apt-get install -q -y make g++ file - run: | - cd /trimal/source && make all && file trimal && file readal && file statal && - cd .. && ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh build_and_test_windows: runs-on: windows-2022 steps: @@ -63,17 +35,6 @@ jobs: Get-Command .\trimAl_Windows_x86-64\readal.exe Get-Command .\trimAl_Windows_x86-64\statal.exe - - name: Check Binary Dependencies - run: | - "C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.28.29910\bin\Hostx64\x64\dumpbin.exe" /DEPENDENTS .\trimAl_Windows_x86-64\trimal.exe - - name: Run Tests on Binaries - continue-on-error: true - run: | - .\trimAl_Windows_x86-64\trimal.exe --help 2>&1 | tee trimal_help.txt - - - name: Display Logs - if: failure() run: | - echo trimal.exe --help output: - type trimal_help.txt + .\trimAl_Windows_x86-64\trimal.exe --help From 742fd6607fcd37c37bdb870fec917476a173c07f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:23:44 +0200 Subject: [PATCH 10/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 1f9a8f15a..30096e3de 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched. +Temporary file to force Github Actions workflow to be launched From 47bd36ca1ec0e08d1eca46f0b08d39346872109c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:28:24 +0200 Subject: [PATCH 11/61] List directory --- .github/workflows/build.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 43c38461f..62d794645 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -26,6 +26,7 @@ jobs: powershell -Command "Expand-Archive -Path trimal.zip -DestinationPath ." - name: List Directory Contents run: | + dir .\ dir .\trimAl_Windows_x86-64\ - name: Verify Binaries From 8bdb6cb2eb2ac32a9de67d290cb452bb8979dc79 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:28:37 +0200 Subject: [PATCH 12/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 30096e3de..1f9a8f15a 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched +Temporary file to force Github Actions workflow to be launched. From 4dd8840eebc206b438eea183cee500d2c626f39a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:30:09 +0200 Subject: [PATCH 13/61] Fix binaries path --- .github/workflows/build.yml | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 62d794645..73925a120 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -27,15 +27,12 @@ jobs: - name: List Directory Contents run: | dir .\ - dir .\trimAl_Windows_x86-64\ - name: Verify Binaries run: | # Use PowerShell or native Windows commands to verify binaries - Get-Command .\trimAl_Windows_x86-64\trimal.exe - Get-Command .\trimAl_Windows_x86-64\readal.exe - Get-Command .\trimAl_Windows_x86-64\statal.exe + Get-Command .\trimal.exe - name: Run Tests on Binaries run: | - .\trimAl_Windows_x86-64\trimal.exe --help + .\trimal.exe --help From 53f8563886f9dddaea7289cc1fe9ab473b2bf237 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:30:19 +0200 Subject: [PATCH 14/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 1f9a8f15a..30096e3de 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched. +Temporary file to force Github Actions workflow to be launched From d43cc136af1d156348825a644d9f735095aae29e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:32:40 +0200 Subject: [PATCH 15/61] Remove non-existent parameter --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 73925a120..27d789f23 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -35,4 +35,4 @@ jobs: - name: Run Tests on Binaries run: | - .\trimal.exe --help + .\trimal.exe From 0731e9c7600d111aee917532af7bb0f3f942ad34 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:32:52 +0200 Subject: [PATCH 16/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 30096e3de..1f9a8f15a 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched +Temporary file to force Github Actions workflow to be launched. From e80720a67851d2ead36f47c7df731392e6bb5b22 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:52:38 +0200 Subject: [PATCH 17/61] Add generate_trimmed_msas Power Shell script --- scripts/generate_trimmed_msas.ps1 | 514 ++++++++++++++++++++++++++++++ 1 file changed, 514 insertions(+) create mode 100644 scripts/generate_trimmed_msas.ps1 diff --git a/scripts/generate_trimmed_msas.ps1 b/scripts/generate_trimmed_msas.ps1 new file mode 100644 index 000000000..be61da6f6 --- /dev/null +++ b/scripts/generate_trimmed_msas.ps1 @@ -0,0 +1,514 @@ +# Create directories +New-Item -ItemType Directory -Path "test_msas" +New-Item -ItemType Directory -Path "test_msas\gappyout" +New-Item -ItemType Directory -Path "test_msas\strict" +New-Item -ItemType Directory -Path "test_msas\strictplus" +New-Item -ItemType Directory -Path "test_msas\automated1" +New-Item -ItemType Directory -Path "test_msas\nogaps" +New-Item -ItemType Directory -Path "test_msas\noallgaps" + +# Run trimal commands +.\trimal.exe -in dataset\example.004.AA.fasta -gappyout > test_msas\gappyout\example.004.AA.fasta +.\trimal.exe -in dataset\example.004.AA.fasta -strict > test_msas\strict\example.004.AA.fasta +.\trimal.exe -in dataset\example.004.AA.fasta -strictplus > test_msas\strictplus\example.004.AA.fasta +.\trimal.exe -in dataset\example.004.AA.fasta -automated1 > test_msas\automated1\example.004.AA.fasta +.\trimal.exe -in dataset\example.004.AA.fasta -nogaps > test_msas\nogaps\example.004.AA.fasta +.\trimal.exe -in dataset\example.004.AA.fasta -noallgaps > test_msas\noallgaps\example.004.AA.fasta +.\trimal.exe -in dataset\example.005.AA.fasta -gappyout > test_msas\gappyout\example.005.AA.fasta +.\trimal.exe -in dataset\example.005.AA.fasta -strict > test_msas\strict\example.005.AA.fasta +.\trimal.exe -in dataset\example.005.AA.fasta -strictplus > test_msas\strictplus\example.005.AA.fasta +.\trimal.exe -in dataset\example.005.AA.fasta -automated1 > test_msas\automated1\example.005.AA.fasta +.\trimal.exe -in dataset\example.005.AA.fasta -nogaps > test_msas\nogaps\example.005.AA.fasta +.\trimal.exe -in dataset\example.005.AA.fasta -noallgaps > test_msas\noallgaps\example.005.AA.fasta +.\trimal.exe -in dataset\example.007.AA.fasta -gappyout > test_msas\gappyout\example.007.AA.fasta +.\trimal.exe -in dataset\example.007.AA.fasta -strict > test_msas\strict\example.007.AA.fasta +.\trimal.exe -in dataset\example.007.AA.fasta -strictplus > test_msas\strictplus\example.007.AA.fasta +.\trimal.exe -in dataset\example.007.AA.fasta -automated1 > test_msas\automated1\example.007.AA.fasta +.\trimal.exe -in dataset\example.007.AA.fasta -nogaps > test_msas\nogaps\example.007.AA.fasta +.\trimal.exe -in dataset\example.007.AA.fasta -noallgaps > test_msas\noallgaps\example.007.AA.fasta +.\trimal.exe -in dataset\example.009.AA.fasta -gappyout > test_msas\gappyout\example.009.AA.fasta +.\trimal.exe -in dataset\example.009.AA.fasta -strict > test_msas\strict\example.009.AA.fasta +.\trimal.exe -in dataset\example.009.AA.fasta -strictplus > test_msas\strictplus\example.009.AA.fasta +.\trimal.exe -in dataset\example.009.AA.fasta -automated1 > test_msas\automated1\example.009.AA.fasta +.\trimal.exe -in dataset\example.009.AA.fasta -nogaps > test_msas\nogaps\example.009.AA.fasta +.\trimal.exe -in dataset\example.009.AA.fasta -noallgaps > test_msas\noallgaps\example.009.AA.fasta +.\trimal.exe -in dataset\example.010.AA.fasta -gappyout > test_msas\gappyout\example.010.AA.fasta +.\trimal.exe -in dataset\example.010.AA.fasta -strict > test_msas\strict\example.010.AA.fasta +.\trimal.exe -in dataset\example.010.AA.fasta -strictplus > test_msas\strictplus\example.010.AA.fasta +.\trimal.exe -in dataset\example.010.AA.fasta -automated1 > test_msas\automated1\example.010.AA.fasta +.\trimal.exe -in dataset\example.010.AA.fasta -nogaps > test_msas\nogaps\example.010.AA.fasta +.\trimal.exe -in dataset\example.010.AA.fasta -noallgaps > test_msas\noallgaps\example.010.AA.fasta +.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -gappyout > test_msas\gappyout\example.011.AA.YKL197C.fasta +.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -strict > test_msas\strict\example.011.AA.YKL197C.fasta +.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -strictplus > test_msas\strictplus\example.011.AA.YKL197C.fasta +.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -automated1 > test_msas\automated1\example.011.AA.YKL197C.fasta +.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -nogaps > test_msas\nogaps\example.011.AA.YKL197C.fasta +.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -noallgaps > test_msas\noallgaps\example.011.AA.YKL197C.fasta +.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -gappyout > test_msas\gappyout\example.014.AA.EggNOG.COG0591.fasta +.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -strict > test_msas\strict\example.014.AA.EggNOG.COG0591.fasta +.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -strictplus > test_msas\strictplus\example.014.AA.EggNOG.COG0591.fasta +.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -automated1 > test_msas\automated1\example.014.AA.EggNOG.COG0591.fasta +.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -nogaps > test_msas\nogaps\example.014.AA.EggNOG.COG0591.fasta +.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -noallgaps > test_msas\noallgaps\example.014.AA.EggNOG.COG0591.fasta +.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -gappyout > test_msas\gappyout\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -strict > test_msas\strict\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -strictplus > test_msas\strictplus\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -automated1 > test_msas\automated1\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -nogaps > test_msas\nogaps\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -noallgaps > test_msas\noallgaps\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -gappyout > test_msas\gappyout\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -strict > test_msas\strict\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -strictplus > test_msas\strictplus\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -automated1 > test_msas\automated1\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -nogaps > test_msas\nogaps\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -noallgaps > test_msas\noallgaps\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -gappyout > test_msas\gappyout\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -strict > test_msas\strict\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -strictplus > test_msas\strictplus\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -automated1 > test_msas\automated1\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -nogaps > test_msas\nogaps\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -noallgaps > test_msas\noallgaps\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -gappyout > test_msas\gappyout\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -strict > test_msas\strict\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -strictplus > test_msas\strictplus\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -automated1 > test_msas\automated1\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -nogaps > test_msas\nogaps\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -noallgaps > test_msas\noallgaps\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -gappyout > test_msas\gappyout\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -strict > test_msas\strict\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -strictplus > test_msas\strictplus\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -automated1 > test_msas\automated1\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -nogaps > test_msas\nogaps\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -noallgaps > test_msas\noallgaps\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -gappyout > test_msas\gappyout\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -strict > test_msas\strict\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -strictplus > test_msas\strictplus\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -automated1 > test_msas\automated1\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -nogaps > test_msas\nogaps\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -noallgaps > test_msas\noallgaps\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -gappyout > test_msas\gappyout\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -strict > test_msas\strict\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -strictplus > test_msas\strictplus\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -automated1 > test_msas\automated1\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -nogaps > test_msas\nogaps\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -noallgaps > test_msas\noallgaps\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -gappyout > test_msas\gappyout\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -strict > test_msas\strict\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -strictplus > test_msas\strictplus\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -automated1 > test_msas\automated1\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -nogaps > test_msas\nogaps\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -noallgaps > test_msas\noallgaps\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -gappyout > test_msas\gappyout\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -strict > test_msas\strict\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -strictplus > test_msas\strictplus\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -automated1 > test_msas\automated1\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -nogaps > test_msas\nogaps\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -noallgaps > test_msas\noallgaps\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -gappyout > test_msas\gappyout\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -strict > test_msas\strict\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -strictplus > test_msas\strictplus\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -automated1 > test_msas\automated1\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -nogaps > test_msas\nogaps\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -noallgaps > test_msas\noallgaps\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -gappyout > test_msas\gappyout\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -strict > test_msas\strict\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -strictplus > test_msas\strictplus\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -automated1 > test_msas\automated1\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -nogaps > test_msas\nogaps\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -noallgaps > test_msas\noallgaps\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -gappyout > test_msas\gappyout\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -strict > test_msas\strict\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -strictplus > test_msas\strictplus\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -automated1 > test_msas\automated1\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -nogaps > test_msas\nogaps\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -noallgaps > test_msas\noallgaps\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -gappyout > test_msas\gappyout\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -strict > test_msas\strict\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -strictplus > test_msas\strictplus\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -automated1 > test_msas\automated1\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -nogaps > test_msas\nogaps\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -noallgaps > test_msas\noallgaps\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -gappyout > test_msas\gappyout\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -strict > test_msas\strict\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -strictplus > test_msas\strictplus\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -automated1 > test_msas\automated1\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -nogaps > test_msas\nogaps\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -noallgaps > test_msas\noallgaps\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -gappyout > test_msas\gappyout\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -strict > test_msas\strict\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -strictplus > test_msas\strictplus\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -automated1 > test_msas\automated1\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -nogaps > test_msas\nogaps\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -noallgaps > test_msas\noallgaps\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -gappyout > test_msas\gappyout\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -strict > test_msas\strict\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -strictplus > test_msas\strictplus\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -automated1 > test_msas\automated1\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -nogaps > test_msas\nogaps\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -noallgaps > test_msas\noallgaps\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -gappyout > test_msas\gappyout\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -strict > test_msas\strict\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -strictplus > test_msas\strictplus\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -automated1 > test_msas\automated1\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -nogaps > test_msas\nogaps\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -noallgaps > test_msas\noallgaps\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -gappyout > test_msas\gappyout\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -strict > test_msas\strict\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -strictplus > test_msas\strictplus\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -automated1 > test_msas\automated1\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -nogaps > test_msas\nogaps\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -noallgaps > test_msas\noallgaps\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -gappyout > test_msas\gappyout\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -strict > test_msas\strict\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -strictplus > test_msas\strictplus\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -automated1 > test_msas\automated1\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -nogaps > test_msas\nogaps\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -noallgaps > test_msas\noallgaps\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -gappyout > test_msas\gappyout\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -strict > test_msas\strict\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -strictplus > test_msas\strictplus\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -automated1 > test_msas\automated1\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -nogaps > test_msas\nogaps\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -noallgaps > test_msas\noallgaps\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -gappyout > test_msas\gappyout\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -strict > test_msas\strict\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -strictplus > test_msas\strictplus\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -automated1 > test_msas\automated1\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -nogaps > test_msas\nogaps\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -noallgaps > test_msas\noallgaps\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -gappyout > test_msas\gappyout\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -strict > test_msas\strict\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -strictplus > test_msas\strictplus\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -automated1 > test_msas\automated1\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -nogaps > test_msas\nogaps\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -noallgaps > test_msas\noallgaps\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -gappyout > test_msas\gappyout\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -strict > test_msas\strict\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -strictplus > test_msas\strictplus\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -automated1 > test_msas\automated1\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -nogaps > test_msas\nogaps\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -noallgaps > test_msas\noallgaps\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -gappyout > test_msas\gappyout\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -strict > test_msas\strict\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -strictplus > test_msas\strictplus\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -automated1 > test_msas\automated1\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -nogaps > test_msas\nogaps\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -noallgaps > test_msas\noallgaps\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -gappyout > test_msas\gappyout\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -strict > test_msas\strict\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -strictplus > test_msas\strictplus\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -automated1 > test_msas\automated1\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -nogaps > test_msas\nogaps\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -noallgaps > test_msas\noallgaps\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -gappyout > test_msas\gappyout\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -strict > test_msas\strict\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -strictplus > test_msas\strictplus\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -automated1 > test_msas\automated1\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -nogaps > test_msas\nogaps\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -noallgaps > test_msas\noallgaps\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -gappyout > test_msas\gappyout\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -strict > test_msas\strict\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -strictplus > test_msas\strictplus\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -automated1 > test_msas\automated1\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -nogaps > test_msas\nogaps\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -noallgaps > test_msas\noallgaps\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -gappyout > test_msas\gappyout\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -strict > test_msas\strict\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -strictplus > test_msas\strictplus\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -automated1 > test_msas\automated1\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -nogaps > test_msas\nogaps\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -noallgaps > test_msas\noallgaps\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -gappyout > test_msas\gappyout\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -strict > test_msas\strict\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -strictplus > test_msas\strictplus\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -automated1 > test_msas\automated1\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -nogaps > test_msas\nogaps\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -noallgaps > test_msas\noallgaps\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -gappyout > test_msas\gappyout\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -strict > test_msas\strict\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -strictplus > test_msas\strictplus\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -automated1 > test_msas\automated1\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -nogaps > test_msas\nogaps\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -noallgaps > test_msas\noallgaps\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -gappyout > test_msas\gappyout\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -strict > test_msas\strict\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -strictplus > test_msas\strictplus\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -automated1 > test_msas\automated1\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -nogaps > test_msas\nogaps\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -noallgaps > test_msas\noallgaps\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -gappyout > test_msas\gappyout\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -strict > test_msas\strict\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -strictplus > test_msas\strictplus\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -automated1 > test_msas\automated1\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -nogaps > test_msas\nogaps\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -noallgaps > test_msas\noallgaps\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -gappyout > test_msas\gappyout\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -strict > test_msas\strict\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -strictplus > test_msas\strictplus\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -automated1 > test_msas\automated1\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -nogaps > test_msas\nogaps\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -noallgaps > test_msas\noallgaps\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -gappyout > test_msas\gappyout\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strict > test_msas\strict\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strictplus > test_msas\strictplus\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -automated1 > test_msas\automated1\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -nogaps > test_msas\nogaps\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -noallgaps > test_msas\noallgaps\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -gappyout > test_msas\gappyout\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -strict > test_msas\strict\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -strictplus > test_msas\strictplus\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -automated1 > test_msas\automated1\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -nogaps > test_msas\nogaps\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -noallgaps > test_msas\noallgaps\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -gappyout > test_msas\gappyout\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strict > test_msas\strict\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strictplus > test_msas\strictplus\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -automated1 > test_msas\automated1\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -nogaps > test_msas\nogaps\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -noallgaps > test_msas\noallgaps\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -gappyout > test_msas\gappyout\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strict > test_msas\strict\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strictplus > test_msas\strictplus\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -automated1 > test_msas\automated1\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -nogaps > test_msas\nogaps\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -noallgaps > test_msas\noallgaps\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -gappyout > test_msas\gappyout\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -strict > test_msas\strict\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -strictplus > test_msas\strictplus\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -automated1 > test_msas\automated1\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -nogaps > test_msas\nogaps\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -noallgaps > test_msas\noallgaps\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -gappyout > test_msas\gappyout\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -strict > test_msas\strict\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -strictplus > test_msas\strictplus\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -automated1 > test_msas\automated1\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -nogaps > test_msas\nogaps\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -noallgaps > test_msas\noallgaps\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -gappyout > test_msas\gappyout\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -strict > test_msas\strict\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -strictplus > test_msas\strictplus\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -automated1 > test_msas\automated1\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -nogaps > test_msas\nogaps\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -noallgaps > test_msas\noallgaps\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -gappyout > test_msas\gappyout\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -strict > test_msas\strict\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -strictplus > test_msas\strictplus\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -automated1 > test_msas\automated1\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -nogaps > test_msas\nogaps\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -noallgaps > test_msas\noallgaps\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -gappyout > test_msas\gappyout\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strict > test_msas\strict\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strictplus > test_msas\strictplus\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -automated1 > test_msas\automated1\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -nogaps > test_msas\nogaps\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -noallgaps > test_msas\noallgaps\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -gappyout > test_msas\gappyout\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strict > test_msas\strict\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strictplus > test_msas\strictplus\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -automated1 > test_msas\automated1\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -nogaps > test_msas\nogaps\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -noallgaps > test_msas\noallgaps\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -gappyout > test_msas\gappyout\example.058.AA.strNOG.ENOG411BBR6.fasta +.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -strict > test_msas\strict\example.058.AA.strNOG.ENOG411BBR6.fasta +.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -strictplus > test_msas\strictplus\example.058.AA.strNOG.ENOG411BBR6.fasta +.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -automated1 > test_msas\automated1\example.058.AA.strNOG.ENOG411BBR6.fasta +.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -nogaps > test_msas\nogaps\example.058.AA.strNOG.ENOG411BBR6.fasta +.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -noallgaps > test_msas\noallgaps\example.058.AA.strNOG.ENOG411BBR6.fasta +.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -gappyout > test_msas\gappyout\example.059.AA.strNOG.ENOG411BBRR.fasta +.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -strict > test_msas\strict\example.059.AA.strNOG.ENOG411BBRR.fasta +.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -strictplus > test_msas\strictplus\example.059.AA.strNOG.ENOG411BBRR.fasta +.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -automated1 > test_msas\automated1\example.059.AA.strNOG.ENOG411BBRR.fasta +.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -nogaps > test_msas\nogaps\example.059.AA.strNOG.ENOG411BBRR.fasta +.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -noallgaps > test_msas\noallgaps\example.059.AA.strNOG.ENOG411BBRR.fasta +.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -gappyout > test_msas\gappyout\example.060.AA.strNOG.ENOG411BBWK.fasta +.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -strict > test_msas\strict\example.060.AA.strNOG.ENOG411BBWK.fasta +.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -strictplus > test_msas\strictplus\example.060.AA.strNOG.ENOG411BBWK.fasta +.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -automated1 > test_msas\automated1\example.060.AA.strNOG.ENOG411BBWK.fasta +.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -nogaps > test_msas\nogaps\example.060.AA.strNOG.ENOG411BBWK.fasta +.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -noallgaps > test_msas\noallgaps\example.060.AA.strNOG.ENOG411BBWK.fasta +.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -gappyout > test_msas\gappyout\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -strict > test_msas\strict\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -strictplus > test_msas\strictplus\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -automated1 > test_msas\automated1\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -nogaps > test_msas\nogaps\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -noallgaps > test_msas\noallgaps\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -gappyout > test_msas\gappyout\example.062.AA.strNOG.ENOG411BCX3.fasta +.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -strict > test_msas\strict\example.062.AA.strNOG.ENOG411BCX3.fasta +.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -strictplus > test_msas\strictplus\example.062.AA.strNOG.ENOG411BCX3.fasta +.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -automated1 > test_msas\automated1\example.062.AA.strNOG.ENOG411BCX3.fasta +.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -nogaps > test_msas\nogaps\example.062.AA.strNOG.ENOG411BCX3.fasta +.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -noallgaps > test_msas\noallgaps\example.062.AA.strNOG.ENOG411BCX3.fasta +.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -gappyout > test_msas\gappyout\example.063.AA.strNOG.ENOG411BDBU.fasta +.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -strict > test_msas\strict\example.063.AA.strNOG.ENOG411BDBU.fasta +.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -strictplus > test_msas\strictplus\example.063.AA.strNOG.ENOG411BDBU.fasta +.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -automated1 > test_msas\automated1\example.063.AA.strNOG.ENOG411BDBU.fasta +.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -nogaps > test_msas\nogaps\example.063.AA.strNOG.ENOG411BDBU.fasta +.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -noallgaps > test_msas\noallgaps\example.063.AA.strNOG.ENOG411BDBU.fasta +.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -gappyout > test_msas\gappyout\example.064.AA.strNOG.ENOG411BDKC.fasta +.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -strict > test_msas\strict\example.064.AA.strNOG.ENOG411BDKC.fasta +.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -strictplus > test_msas\strictplus\example.064.AA.strNOG.ENOG411BDKC.fasta +.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -automated1 > test_msas\automated1\example.064.AA.strNOG.ENOG411BDKC.fasta +.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -nogaps > test_msas\nogaps\example.064.AA.strNOG.ENOG411BDKC.fasta +.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -noallgaps > test_msas\noallgaps\example.064.AA.strNOG.ENOG411BDKC.fasta +.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -gappyout > test_msas\gappyout\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -strict > test_msas\strict\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -strictplus > test_msas\strictplus\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -automated1 > test_msas\automated1\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -nogaps > test_msas\nogaps\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -noallgaps > test_msas\noallgaps\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -gappyout > test_msas\gappyout\example.066.AA.strNOG.ENOG411BDUE.fasta +.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -strict > test_msas\strict\example.066.AA.strNOG.ENOG411BDUE.fasta +.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -strictplus > test_msas\strictplus\example.066.AA.strNOG.ENOG411BDUE.fasta +.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -automated1 > test_msas\automated1\example.066.AA.strNOG.ENOG411BDUE.fasta +.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -nogaps > test_msas\nogaps\example.066.AA.strNOG.ENOG411BDUE.fasta +.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -noallgaps > test_msas\noallgaps\example.066.AA.strNOG.ENOG411BDUE.fasta +.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -gappyout > test_msas\gappyout\example.067.AA.strNOG.ENOG411BDX3.fasta +.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -strict > test_msas\strict\example.067.AA.strNOG.ENOG411BDX3.fasta +.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -strictplus > test_msas\strictplus\example.067.AA.strNOG.ENOG411BDX3.fasta +.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -automated1 > test_msas\automated1\example.067.AA.strNOG.ENOG411BDX3.fasta +.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -nogaps > test_msas\nogaps\example.067.AA.strNOG.ENOG411BDX3.fasta +.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -noallgaps > test_msas\noallgaps\example.067.AA.strNOG.ENOG411BDX3.fasta +.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -gappyout > test_msas\gappyout\example.068.AA.strNOG.ENOG411BE45.fasta +.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -strict > test_msas\strict\example.068.AA.strNOG.ENOG411BE45.fasta +.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -strictplus > test_msas\strictplus\example.068.AA.strNOG.ENOG411BE45.fasta +.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -automated1 > test_msas\automated1\example.068.AA.strNOG.ENOG411BE45.fasta +.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -nogaps > test_msas\nogaps\example.068.AA.strNOG.ENOG411BE45.fasta +.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -noallgaps > test_msas\noallgaps\example.068.AA.strNOG.ENOG411BE45.fasta +.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -gappyout > test_msas\gappyout\example.069.AA.strNOG.ENOG411BE8B.fasta +.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -strict > test_msas\strict\example.069.AA.strNOG.ENOG411BE8B.fasta +.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -strictplus > test_msas\strictplus\example.069.AA.strNOG.ENOG411BE8B.fasta +.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -automated1 > test_msas\automated1\example.069.AA.strNOG.ENOG411BE8B.fasta +.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -nogaps > test_msas\nogaps\example.069.AA.strNOG.ENOG411BE8B.fasta +.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -noallgaps > test_msas\noallgaps\example.069.AA.strNOG.ENOG411BE8B.fasta +.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -gappyout > test_msas\gappyout\example.070.AA.strNOG.ENOG411BEUV.fasta +.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -strict > test_msas\strict\example.070.AA.strNOG.ENOG411BEUV.fasta +.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -strictplus > test_msas\strictplus\example.070.AA.strNOG.ENOG411BEUV.fasta +.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -automated1 > test_msas\automated1\example.070.AA.strNOG.ENOG411BEUV.fasta +.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -nogaps > test_msas\nogaps\example.070.AA.strNOG.ENOG411BEUV.fasta +.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -noallgaps > test_msas\noallgaps\example.070.AA.strNOG.ENOG411BEUV.fasta +.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -gappyout > test_msas\gappyout\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -strict > test_msas\strict\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -strictplus > test_msas\strictplus\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -automated1 > test_msas\automated1\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -nogaps > test_msas\nogaps\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -noallgaps > test_msas\noallgaps\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -gappyout > test_msas\gappyout\example.072.AA.strNOG.ENOG411BF1S.fasta +.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -strict > test_msas\strict\example.072.AA.strNOG.ENOG411BF1S.fasta +.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -strictplus > test_msas\strictplus\example.072.AA.strNOG.ENOG411BF1S.fasta +.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -automated1 > test_msas\automated1\example.072.AA.strNOG.ENOG411BF1S.fasta +.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -nogaps > test_msas\nogaps\example.072.AA.strNOG.ENOG411BF1S.fasta +.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -noallgaps > test_msas\noallgaps\example.072.AA.strNOG.ENOG411BF1S.fasta +.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -gappyout > test_msas\gappyout\example.073.AA.strNOG.ENOG411BFCW.fasta +.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -strict > test_msas\strict\example.073.AA.strNOG.ENOG411BFCW.fasta +.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -strictplus > test_msas\strictplus\example.073.AA.strNOG.ENOG411BFCW.fasta +.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -automated1 > test_msas\automated1\example.073.AA.strNOG.ENOG411BFCW.fasta +.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -nogaps > test_msas\nogaps\example.073.AA.strNOG.ENOG411BFCW.fasta +.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -noallgaps > test_msas\noallgaps\example.073.AA.strNOG.ENOG411BFCW.fasta +.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -gappyout > test_msas\gappyout\example.074.AA.strNOG.ENOG411BFPF.fasta +.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -strict > test_msas\strict\example.074.AA.strNOG.ENOG411BFPF.fasta +.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -strictplus > test_msas\strictplus\example.074.AA.strNOG.ENOG411BFPF.fasta +.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -automated1 > test_msas\automated1\example.074.AA.strNOG.ENOG411BFPF.fasta +.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -nogaps > test_msas\nogaps\example.074.AA.strNOG.ENOG411BFPF.fasta +.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -noallgaps > test_msas\noallgaps\example.074.AA.strNOG.ENOG411BFPF.fasta +.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -gappyout > test_msas\gappyout\example.075.AA.strNOG.ENOG411BFQS.fasta +.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -strict > test_msas\strict\example.075.AA.strNOG.ENOG411BFQS.fasta +.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -strictplus > test_msas\strictplus\example.075.AA.strNOG.ENOG411BFQS.fasta +.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -automated1 > test_msas\automated1\example.075.AA.strNOG.ENOG411BFQS.fasta +.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -nogaps > test_msas\nogaps\example.075.AA.strNOG.ENOG411BFQS.fasta +.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -noallgaps > test_msas\noallgaps\example.075.AA.strNOG.ENOG411BFQS.fasta +.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -gappyout > test_msas\gappyout\example.076.AA.strNOG.ENOG411BH75.fasta +.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -strict > test_msas\strict\example.076.AA.strNOG.ENOG411BH75.fasta +.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -strictplus > test_msas\strictplus\example.076.AA.strNOG.ENOG411BH75.fasta +.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -automated1 > test_msas\automated1\example.076.AA.strNOG.ENOG411BH75.fasta +.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -nogaps > test_msas\nogaps\example.076.AA.strNOG.ENOG411BH75.fasta +.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -noallgaps > test_msas\noallgaps\example.076.AA.strNOG.ENOG411BH75.fasta +.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -gappyout > test_msas\gappyout\example.077.AA.strNOG.ENOG411BH79.fasta +.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -strict > test_msas\strict\example.077.AA.strNOG.ENOG411BH79.fasta +.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -strictplus > test_msas\strictplus\example.077.AA.strNOG.ENOG411BH79.fasta +.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -automated1 > test_msas\automated1\example.077.AA.strNOG.ENOG411BH79.fasta +.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -nogaps > test_msas\nogaps\example.077.AA.strNOG.ENOG411BH79.fasta +.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -noallgaps > test_msas\noallgaps\example.077.AA.strNOG.ENOG411BH79.fasta +.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -gappyout > test_msas\gappyout\example.078.AA.strNOG.ENOG411BH99.fasta +.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -strict > test_msas\strict\example.078.AA.strNOG.ENOG411BH99.fasta +.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -strictplus > test_msas\strictplus\example.078.AA.strNOG.ENOG411BH99.fasta +.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -automated1 > test_msas\automated1\example.078.AA.strNOG.ENOG411BH99.fasta +.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -nogaps > test_msas\nogaps\example.078.AA.strNOG.ENOG411BH99.fasta +.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -noallgaps > test_msas\noallgaps\example.078.AA.strNOG.ENOG411BH99.fasta +.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -gappyout > test_msas\gappyout\example.079.AA.strNOG.ENOG411BJDC.fasta +.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -strict > test_msas\strict\example.079.AA.strNOG.ENOG411BJDC.fasta +.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -strictplus > test_msas\strictplus\example.079.AA.strNOG.ENOG411BJDC.fasta +.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -automated1 > test_msas\automated1\example.079.AA.strNOG.ENOG411BJDC.fasta +.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -nogaps > test_msas\nogaps\example.079.AA.strNOG.ENOG411BJDC.fasta +.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -noallgaps > test_msas\noallgaps\example.079.AA.strNOG.ENOG411BJDC.fasta +.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -gappyout > test_msas\gappyout\example.080.AA.strNOG.ENOG411BJIF.fasta +.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -strict > test_msas\strict\example.080.AA.strNOG.ENOG411BJIF.fasta +.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -strictplus > test_msas\strictplus\example.080.AA.strNOG.ENOG411BJIF.fasta +.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -automated1 > test_msas\automated1\example.080.AA.strNOG.ENOG411BJIF.fasta +.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -nogaps > test_msas\nogaps\example.080.AA.strNOG.ENOG411BJIF.fasta +.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -noallgaps > test_msas\noallgaps\example.080.AA.strNOG.ENOG411BJIF.fasta +.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -gappyout > test_msas\gappyout\example.081.AA.strNOG.ENOG411BK9X.fasta +.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -strict > test_msas\strict\example.081.AA.strNOG.ENOG411BK9X.fasta +.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -strictplus > test_msas\strictplus\example.081.AA.strNOG.ENOG411BK9X.fasta +.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -automated1 > test_msas\automated1\example.081.AA.strNOG.ENOG411BK9X.fasta +.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -nogaps > test_msas\nogaps\example.081.AA.strNOG.ENOG411BK9X.fasta +.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -noallgaps > test_msas\noallgaps\example.081.AA.strNOG.ENOG411BK9X.fasta +.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -gappyout > test_msas\gappyout\example.082.AA.strNOG.ENOG411BKC5.fasta +.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -strict > test_msas\strict\example.082.AA.strNOG.ENOG411BKC5.fasta +.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -strictplus > test_msas\strictplus\example.082.AA.strNOG.ENOG411BKC5.fasta +.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -automated1 > test_msas\automated1\example.082.AA.strNOG.ENOG411BKC5.fasta +.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -nogaps > test_msas\nogaps\example.082.AA.strNOG.ENOG411BKC5.fasta +.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -noallgaps > test_msas\noallgaps\example.082.AA.strNOG.ENOG411BKC5.fasta +.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -gappyout > test_msas\gappyout\example.083.AA.strNOG.ENOG411BMKC.fasta +.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -strict > test_msas\strict\example.083.AA.strNOG.ENOG411BMKC.fasta +.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -strictplus > test_msas\strictplus\example.083.AA.strNOG.ENOG411BMKC.fasta +.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -automated1 > test_msas\automated1\example.083.AA.strNOG.ENOG411BMKC.fasta +.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -nogaps > test_msas\nogaps\example.083.AA.strNOG.ENOG411BMKC.fasta +.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -noallgaps > test_msas\noallgaps\example.083.AA.strNOG.ENOG411BMKC.fasta +.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -gappyout > test_msas\gappyout\example.084.AA.strNOG.ENOG411BNP9.fasta +.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -strict > test_msas\strict\example.084.AA.strNOG.ENOG411BNP9.fasta +.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -strictplus > test_msas\strictplus\example.084.AA.strNOG.ENOG411BNP9.fasta +.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -automated1 > test_msas\automated1\example.084.AA.strNOG.ENOG411BNP9.fasta +.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -nogaps > test_msas\nogaps\example.084.AA.strNOG.ENOG411BNP9.fasta +.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -noallgaps > test_msas\noallgaps\example.084.AA.strNOG.ENOG411BNP9.fasta +.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -gappyout > test_msas\gappyout\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -strict > test_msas\strict\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -strictplus > test_msas\strictplus\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -automated1 > test_msas\automated1\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -nogaps > test_msas\nogaps\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -noallgaps > test_msas\noallgaps\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -gappyout > test_msas\gappyout\example.086.AA.strNOG.ENOG411BR1D.fasta +.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -strict > test_msas\strict\example.086.AA.strNOG.ENOG411BR1D.fasta +.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -strictplus > test_msas\strictplus\example.086.AA.strNOG.ENOG411BR1D.fasta +.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -automated1 > test_msas\automated1\example.086.AA.strNOG.ENOG411BR1D.fasta +.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -nogaps > test_msas\nogaps\example.086.AA.strNOG.ENOG411BR1D.fasta +.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -noallgaps > test_msas\noallgaps\example.086.AA.strNOG.ENOG411BR1D.fasta +.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -gappyout > test_msas\gappyout\example.087.AA.strNOG.ENOG411BRCH.fasta +.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -strict > test_msas\strict\example.087.AA.strNOG.ENOG411BRCH.fasta +.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -strictplus > test_msas\strictplus\example.087.AA.strNOG.ENOG411BRCH.fasta +.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -automated1 > test_msas\automated1\example.087.AA.strNOG.ENOG411BRCH.fasta +.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -nogaps > test_msas\nogaps\example.087.AA.strNOG.ENOG411BRCH.fasta +.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -noallgaps > test_msas\noallgaps\example.087.AA.strNOG.ENOG411BRCH.fasta +.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -gappyout > test_msas\gappyout\example.088.AA.strNOG.ENOG411BSXF.fasta +.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -strict > test_msas\strict\example.088.AA.strNOG.ENOG411BSXF.fasta +.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -strictplus > test_msas\strictplus\example.088.AA.strNOG.ENOG411BSXF.fasta +.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -automated1 > test_msas\automated1\example.088.AA.strNOG.ENOG411BSXF.fasta +.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -nogaps > test_msas\nogaps\example.088.AA.strNOG.ENOG411BSXF.fasta +.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -noallgaps > test_msas\noallgaps\example.088.AA.strNOG.ENOG411BSXF.fasta +.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -gappyout > test_msas\gappyout\example.089.AA.strNOG.ENOG411BV9B.fasta +.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -strict > test_msas\strict\example.089.AA.strNOG.ENOG411BV9B.fasta +.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -strictplus > test_msas\strictplus\example.089.AA.strNOG.ENOG411BV9B.fasta +.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -automated1 > test_msas\automated1\example.089.AA.strNOG.ENOG411BV9B.fasta +.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -nogaps > test_msas\nogaps\example.089.AA.strNOG.ENOG411BV9B.fasta +.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -noallgaps > test_msas\noallgaps\example.089.AA.strNOG.ENOG411BV9B.fasta +.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -gappyout > test_msas\gappyout\example.090.AA.strNOG.ENOG411BVKR.fasta +.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -strict > test_msas\strict\example.090.AA.strNOG.ENOG411BVKR.fasta +.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -strictplus > test_msas\strictplus\example.090.AA.strNOG.ENOG411BVKR.fasta +.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -automated1 > test_msas\automated1\example.090.AA.strNOG.ENOG411BVKR.fasta +.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -nogaps > test_msas\nogaps\example.090.AA.strNOG.ENOG411BVKR.fasta +.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -noallgaps > test_msas\noallgaps\example.090.AA.strNOG.ENOG411BVKR.fasta +.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -gappyout > test_msas\gappyout\example.091.AA.strNOG.ENOG411BWBU.fasta +.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -strict > test_msas\strict\example.091.AA.strNOG.ENOG411BWBU.fasta +.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -strictplus > test_msas\strictplus\example.091.AA.strNOG.ENOG411BWBU.fasta +.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -automated1 > test_msas\automated1\example.091.AA.strNOG.ENOG411BWBU.fasta +.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -nogaps > test_msas\nogaps\example.091.AA.strNOG.ENOG411BWBU.fasta +.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -noallgaps > test_msas\noallgaps\example.091.AA.strNOG.ENOG411BWBU.fasta From ea4de97096f9dbdda9837e086e2c8d048d5c9864 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:52:53 +0200 Subject: [PATCH 18/61] Add compare_trimmed_msas Power Shell script --- scripts/compare_trimmed_msas.ps1 | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 scripts/compare_trimmed_msas.ps1 diff --git a/scripts/compare_trimmed_msas.ps1 b/scripts/compare_trimmed_msas.ps1 new file mode 100644 index 000000000..1a0f54d68 --- /dev/null +++ b/scripts/compare_trimmed_msas.ps1 @@ -0,0 +1,21 @@ +# Define methods +$methods = "gappyout", "strict", "strictplus", "automated1", "nogaps", "noallgaps" + +# Compare files +foreach ($method in $methods) { + $files = Get-ChildItem -Path "test_msas\$method" -Filter *.fasta + foreach ($file in $files) { + $msa_filename = $file.Name + $result = Compare-Object (Get-Content "$file") (Get-Content "dataset\trimmed_msas\$method\$msa_filename") -SyncWindow 0 + if ($result) { + Write-Output "Files $file and dataset\trimmed_msas\$method\$msa_filename differ." + exit 1 + } + else { + Write-Output "Compared $file and dataset\trimmed_msas\$method\$msa_filename" + } + } +} + +# Remove test_msas directory +Remove-Item -Recurse -Force test_msas From 4ecc6637835c5afdcb82e40638a08379e354e3d2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:55:30 +0200 Subject: [PATCH 19/61] Run Windows binaries tests --- .github/workflows/build.yml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 27d789f23..a5ec9246c 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -16,7 +16,7 @@ jobs: build_and_test_windows: runs-on: windows-2022 steps: - #- uses: actions/checkout@v4 + - uses: actions/checkout@v4 - name: Download Release Binaries run: | curl -L -o trimal.zip https://github.com/inab/trimal/releases/download/v1.5.0/trimAl_Windows_x86-64.zip @@ -33,6 +33,10 @@ jobs: # Use PowerShell or native Windows commands to verify binaries Get-Command .\trimal.exe - - name: Run Tests on Binaries + - name: Run generate_trimmed_msas.ps1 run: | - .\trimal.exe + powershell -ExecutionPolicy Bypass -File .\scripts\generate_trimmed_msas.ps1 + + - name: Run compare_trimmed_msas.ps1 + run: | + powershell -ExecutionPolicy Bypass -File .\scripts\compare_trimmed_msas.ps1 From e710557be6d51e54bef62e22c2ec251d15795dfa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 11:55:40 +0200 Subject: [PATCH 20/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 1f9a8f15a..30096e3de 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched. +Temporary file to force Github Actions workflow to be launched From f700c479cf1b67b8ee85d522e69551df19375f15 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 12:24:08 +0200 Subject: [PATCH 21/61] Debug trimmed msa comparisons --- scripts/compare_trimmed_msas.ps1 | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) diff --git a/scripts/compare_trimmed_msas.ps1 b/scripts/compare_trimmed_msas.ps1 index 1a0f54d68..a39ff0469 100644 --- a/scripts/compare_trimmed_msas.ps1 +++ b/scripts/compare_trimmed_msas.ps1 @@ -6,13 +6,26 @@ foreach ($method in $methods) { $files = Get-ChildItem -Path "test_msas\$method" -Filter *.fasta foreach ($file in $files) { $msa_filename = $file.Name - $result = Compare-Object (Get-Content "$file") (Get-Content "dataset\trimmed_msas\$method\$msa_filename") -SyncWindow 0 + $test_file = "$file" + $reference_file = "dataset\trimmed_msas\$method\$msa_filename" + + if (-Not (Test-Path $reference_file)) { + Write-Output "Reference file $reference_file does not exist." + exit 1 + } + + if (-Not (Test-Path $test_file)) { + Write-Output "Test file $test_file does not exist." + exit 1 + } + + $result = Compare-Object (Get-Content $test_file) (Get-Content $reference_file) -SyncWindow 0 if ($result) { - Write-Output "Files $file and dataset\trimmed_msas\$method\$msa_filename differ." + Write-Output "Files $test_file and $reference_file differ." exit 1 } else { - Write-Output "Compared $file and dataset\trimmed_msas\$method\$msa_filename" + Write-Output "Compared $test_file and $reference_file" } } } From a65257fc27c4745788914b116fcf8c69d1f87fc1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 12:39:07 +0200 Subject: [PATCH 22/61] Fix test file paths --- scripts/compare_trimmed_msas.ps1 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/compare_trimmed_msas.ps1 b/scripts/compare_trimmed_msas.ps1 index a39ff0469..b605c5e32 100644 --- a/scripts/compare_trimmed_msas.ps1 +++ b/scripts/compare_trimmed_msas.ps1 @@ -6,8 +6,8 @@ foreach ($method in $methods) { $files = Get-ChildItem -Path "test_msas\$method" -Filter *.fasta foreach ($file in $files) { $msa_filename = $file.Name - $test_file = "$file" - $reference_file = "dataset\trimmed_msas\$method\$msa_filename" + $test_file = $file.FullName + $reference_file = Join-Path -Path "dataset\trimmed_msas\$method" -ChildPath $msa_filename if (-Not (Test-Path $reference_file)) { Write-Output "Reference file $reference_file does not exist." From 3ae8c9a232cd3a21d49c3a8e7c8200ec68da83b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 12:39:58 +0200 Subject: [PATCH 23/61] Simplify tests --- scripts/generate_trimmed_msas.sh | 499 +------------------------------ 1 file changed, 1 insertion(+), 498 deletions(-) diff --git a/scripts/generate_trimmed_msas.sh b/scripts/generate_trimmed_msas.sh index fcc05d90e..5a04008a4 100755 --- a/scripts/generate_trimmed_msas.sh +++ b/scripts/generate_trimmed_msas.sh @@ -12,501 +12,4 @@ mkdir test_msas/noallgaps ./source/trimal -in dataset/example.004.AA.fasta -automated1 > test_msas/automated1/example.004.AA.fasta ./source/trimal -in dataset/example.004.AA.fasta -nogaps > test_msas/nogaps/example.004.AA.fasta ./source/trimal -in dataset/example.004.AA.fasta -noallgaps > test_msas/noallgaps/example.004.AA.fasta -./source/trimal -in dataset/example.005.AA.fasta -gappyout > test_msas/gappyout/example.005.AA.fasta -./source/trimal -in dataset/example.005.AA.fasta -strict > test_msas/strict/example.005.AA.fasta -./source/trimal -in dataset/example.005.AA.fasta -strictplus > test_msas/strictplus/example.005.AA.fasta -./source/trimal -in dataset/example.005.AA.fasta -automated1 > test_msas/automated1/example.005.AA.fasta -./source/trimal -in dataset/example.005.AA.fasta -nogaps > test_msas/nogaps/example.005.AA.fasta -./source/trimal -in dataset/example.005.AA.fasta -noallgaps > test_msas/noallgaps/example.005.AA.fasta -./source/trimal -in dataset/example.007.AA.fasta -gappyout > test_msas/gappyout/example.007.AA.fasta -./source/trimal -in dataset/example.007.AA.fasta -strict > test_msas/strict/example.007.AA.fasta -./source/trimal -in dataset/example.007.AA.fasta -strictplus > test_msas/strictplus/example.007.AA.fasta -./source/trimal -in dataset/example.007.AA.fasta -automated1 > test_msas/automated1/example.007.AA.fasta -./source/trimal -in dataset/example.007.AA.fasta -nogaps > test_msas/nogaps/example.007.AA.fasta -./source/trimal -in dataset/example.007.AA.fasta -noallgaps > test_msas/noallgaps/example.007.AA.fasta -./source/trimal -in dataset/example.009.AA.fasta -gappyout > test_msas/gappyout/example.009.AA.fasta -./source/trimal -in dataset/example.009.AA.fasta -strict > test_msas/strict/example.009.AA.fasta -./source/trimal -in dataset/example.009.AA.fasta -strictplus > test_msas/strictplus/example.009.AA.fasta -./source/trimal -in dataset/example.009.AA.fasta -automated1 > test_msas/automated1/example.009.AA.fasta -./source/trimal -in dataset/example.009.AA.fasta -nogaps > test_msas/nogaps/example.009.AA.fasta -./source/trimal -in dataset/example.009.AA.fasta -noallgaps > test_msas/noallgaps/example.009.AA.fasta -./source/trimal -in dataset/example.010.AA.fasta -gappyout > test_msas/gappyout/example.010.AA.fasta -./source/trimal -in dataset/example.010.AA.fasta -strict > test_msas/strict/example.010.AA.fasta -./source/trimal -in dataset/example.010.AA.fasta -strictplus > test_msas/strictplus/example.010.AA.fasta -./source/trimal -in dataset/example.010.AA.fasta -automated1 > test_msas/automated1/example.010.AA.fasta -./source/trimal -in dataset/example.010.AA.fasta -nogaps > test_msas/nogaps/example.010.AA.fasta -./source/trimal -in dataset/example.010.AA.fasta -noallgaps > test_msas/noallgaps/example.010.AA.fasta -./source/trimal -in dataset/example.011.AA.YKL197C.fasta -gappyout > test_msas/gappyout/example.011.AA.YKL197C.fasta -./source/trimal -in dataset/example.011.AA.YKL197C.fasta -strict > test_msas/strict/example.011.AA.YKL197C.fasta -./source/trimal -in dataset/example.011.AA.YKL197C.fasta -strictplus > test_msas/strictplus/example.011.AA.YKL197C.fasta -./source/trimal -in dataset/example.011.AA.YKL197C.fasta -automated1 > test_msas/automated1/example.011.AA.YKL197C.fasta -./source/trimal -in dataset/example.011.AA.YKL197C.fasta -nogaps > test_msas/nogaps/example.011.AA.YKL197C.fasta -./source/trimal -in dataset/example.011.AA.YKL197C.fasta -noallgaps > test_msas/noallgaps/example.011.AA.YKL197C.fasta -./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -gappyout > test_msas/gappyout/example.014.AA.EggNOG.COG0591.fasta -./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -strict > test_msas/strict/example.014.AA.EggNOG.COG0591.fasta -./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -strictplus > test_msas/strictplus/example.014.AA.EggNOG.COG0591.fasta -./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -automated1 > test_msas/automated1/example.014.AA.EggNOG.COG0591.fasta -./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -nogaps > test_msas/nogaps/example.014.AA.EggNOG.COG0591.fasta -./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -noallgaps > test_msas/noallgaps/example.014.AA.EggNOG.COG0591.fasta -./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -gappyout > test_msas/gappyout/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -strict > test_msas/strict/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -strictplus > test_msas/strictplus/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -automated1 > test_msas/automated1/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -nogaps > test_msas/nogaps/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -noallgaps > test_msas/noallgaps/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -gappyout > test_msas/gappyout/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -strict > test_msas/strict/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -strictplus > test_msas/strictplus/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -automated1 > test_msas/automated1/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -nogaps > test_msas/nogaps/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -noallgaps > test_msas/noallgaps/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -gappyout > test_msas/gappyout/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -strict > test_msas/strict/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -strictplus > test_msas/strictplus/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -automated1 > test_msas/automated1/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -nogaps > test_msas/nogaps/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -noallgaps > test_msas/noallgaps/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -gappyout > test_msas/gappyout/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -strict > test_msas/strict/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -strictplus > test_msas/strictplus/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -automated1 > test_msas/automated1/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -nogaps > test_msas/nogaps/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -noallgaps > test_msas/noallgaps/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -gappyout > test_msas/gappyout/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -strict > test_msas/strict/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -strictplus > test_msas/strictplus/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -automated1 > test_msas/automated1/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -nogaps > test_msas/nogaps/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -noallgaps > test_msas/noallgaps/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -gappyout > test_msas/gappyout/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -strict > test_msas/strict/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -strictplus > test_msas/strictplus/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -automated1 > test_msas/automated1/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -nogaps > test_msas/nogaps/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -noallgaps > test_msas/noallgaps/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -gappyout > test_msas/gappyout/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -strict > test_msas/strict/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -strictplus > test_msas/strictplus/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -automated1 > test_msas/automated1/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -nogaps > test_msas/nogaps/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -noallgaps > test_msas/noallgaps/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -gappyout > test_msas/gappyout/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -strict > test_msas/strict/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -strictplus > test_msas/strictplus/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -automated1 > test_msas/automated1/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -nogaps > test_msas/nogaps/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -noallgaps > test_msas/noallgaps/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -gappyout > test_msas/gappyout/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -strict > test_msas/strict/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -strictplus > test_msas/strictplus/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -automated1 > test_msas/automated1/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -nogaps > test_msas/nogaps/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -noallgaps > test_msas/noallgaps/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -gappyout > test_msas/gappyout/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -strict > test_msas/strict/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -strictplus > test_msas/strictplus/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -automated1 > test_msas/automated1/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -nogaps > test_msas/nogaps/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -noallgaps > test_msas/noallgaps/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -gappyout > test_msas/gappyout/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -strict > test_msas/strict/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -strictplus > test_msas/strictplus/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -automated1 > test_msas/automated1/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -nogaps > test_msas/nogaps/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -noallgaps > test_msas/noallgaps/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -gappyout > test_msas/gappyout/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -strict > test_msas/strict/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -strictplus > test_msas/strictplus/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -automated1 > test_msas/automated1/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -nogaps > test_msas/nogaps/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -noallgaps > test_msas/noallgaps/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -gappyout > test_msas/gappyout/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -strict > test_msas/strict/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -strictplus > test_msas/strictplus/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -automated1 > test_msas/automated1/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -nogaps > test_msas/nogaps/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -noallgaps > test_msas/noallgaps/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -gappyout > test_msas/gappyout/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -strict > test_msas/strict/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -strictplus > test_msas/strictplus/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -automated1 > test_msas/automated1/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -nogaps > test_msas/nogaps/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -noallgaps > test_msas/noallgaps/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -gappyout > test_msas/gappyout/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -strict > test_msas/strict/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -strictplus > test_msas/strictplus/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -automated1 > test_msas/automated1/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -nogaps > test_msas/nogaps/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -noallgaps > test_msas/noallgaps/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -gappyout > test_msas/gappyout/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -strict > test_msas/strict/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -strictplus > test_msas/strictplus/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -automated1 > test_msas/automated1/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -nogaps > test_msas/nogaps/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -noallgaps > test_msas/noallgaps/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -gappyout > test_msas/gappyout/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -strict > test_msas/strict/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -strictplus > test_msas/strictplus/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -automated1 > test_msas/automated1/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -nogaps > test_msas/nogaps/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -noallgaps > test_msas/noallgaps/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -gappyout > test_msas/gappyout/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -strict > test_msas/strict/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -strictplus > test_msas/strictplus/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -automated1 > test_msas/automated1/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -nogaps > test_msas/nogaps/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -noallgaps > test_msas/noallgaps/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -gappyout > test_msas/gappyout/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -strict > test_msas/strict/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -strictplus > test_msas/strictplus/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -automated1 > test_msas/automated1/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -nogaps > test_msas/nogaps/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -noallgaps > test_msas/noallgaps/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -gappyout > test_msas/gappyout/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -strict > test_msas/strict/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -strictplus > test_msas/strictplus/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -automated1 > test_msas/automated1/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -nogaps > test_msas/nogaps/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -noallgaps > test_msas/noallgaps/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -gappyout > test_msas/gappyout/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -strict > test_msas/strict/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -strictplus > test_msas/strictplus/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -automated1 > test_msas/automated1/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -nogaps > test_msas/nogaps/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -noallgaps > test_msas/noallgaps/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -gappyout > test_msas/gappyout/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -strict > test_msas/strict/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -strictplus > test_msas/strictplus/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -automated1 > test_msas/automated1/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -nogaps > test_msas/nogaps/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -noallgaps > test_msas/noallgaps/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -gappyout > test_msas/gappyout/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -strict > test_msas/strict/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -strictplus > test_msas/strictplus/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -automated1 > test_msas/automated1/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -nogaps > test_msas/nogaps/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -noallgaps > test_msas/noallgaps/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -gappyout > test_msas/gappyout/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -strict > test_msas/strict/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -strictplus > test_msas/strictplus/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -automated1 > test_msas/automated1/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -nogaps > test_msas/nogaps/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -noallgaps > test_msas/noallgaps/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -gappyout > test_msas/gappyout/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -strict > test_msas/strict/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -strictplus > test_msas/strictplus/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -automated1 > test_msas/automated1/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -nogaps > test_msas/nogaps/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -noallgaps > test_msas/noallgaps/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -gappyout > test_msas/gappyout/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -strict > test_msas/strict/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -strictplus > test_msas/strictplus/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -automated1 > test_msas/automated1/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -nogaps > test_msas/nogaps/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -noallgaps > test_msas/noallgaps/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -gappyout > test_msas/gappyout/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -strict > test_msas/strict/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -strictplus > test_msas/strictplus/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -automated1 > test_msas/automated1/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -nogaps > test_msas/nogaps/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -noallgaps > test_msas/noallgaps/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -gappyout > test_msas/gappyout/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -strict > test_msas/strict/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -strictplus > test_msas/strictplus/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -automated1 > test_msas/automated1/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -nogaps > test_msas/nogaps/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -noallgaps > test_msas/noallgaps/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -gappyout > test_msas/gappyout/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -strict > test_msas/strict/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -strictplus > test_msas/strictplus/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -automated1 > test_msas/automated1/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -nogaps > test_msas/nogaps/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -noallgaps > test_msas/noallgaps/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -gappyout > test_msas/gappyout/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -strict > test_msas/strict/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -strictplus > test_msas/strictplus/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -automated1 > test_msas/automated1/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -nogaps > test_msas/nogaps/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -noallgaps > test_msas/noallgaps/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -gappyout > test_msas/gappyout/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -strict > test_msas/strict/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -strictplus > test_msas/strictplus/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -automated1 > test_msas/automated1/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -nogaps > test_msas/nogaps/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -noallgaps > test_msas/noallgaps/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -gappyout > test_msas/gappyout/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -strict > test_msas/strict/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -strictplus > test_msas/strictplus/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -automated1 > test_msas/automated1/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -nogaps > test_msas/nogaps/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -noallgaps > test_msas/noallgaps/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -gappyout > test_msas/gappyout/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -strict > test_msas/strict/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -strictplus > test_msas/strictplus/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -automated1 > test_msas/automated1/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -nogaps > test_msas/nogaps/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -noallgaps > test_msas/noallgaps/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -gappyout > test_msas/gappyout/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strict > test_msas/strict/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strictplus > test_msas/strictplus/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -automated1 > test_msas/automated1/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -nogaps > test_msas/nogaps/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -noallgaps > test_msas/noallgaps/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -gappyout > test_msas/gappyout/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -strict > test_msas/strict/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -strictplus > test_msas/strictplus/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -automated1 > test_msas/automated1/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -nogaps > test_msas/nogaps/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -noallgaps > test_msas/noallgaps/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -gappyout > test_msas/gappyout/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strict > test_msas/strict/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strictplus > test_msas/strictplus/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -automated1 > test_msas/automated1/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -nogaps > test_msas/nogaps/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -noallgaps > test_msas/noallgaps/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -gappyout > test_msas/gappyout/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strict > test_msas/strict/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strictplus > test_msas/strictplus/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -automated1 > test_msas/automated1/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -nogaps > test_msas/nogaps/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -noallgaps > test_msas/noallgaps/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -gappyout > test_msas/gappyout/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -strict > test_msas/strict/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -strictplus > test_msas/strictplus/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -automated1 > test_msas/automated1/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -nogaps > test_msas/nogaps/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -noallgaps > test_msas/noallgaps/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -gappyout > test_msas/gappyout/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -strict > test_msas/strict/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -strictplus > test_msas/strictplus/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -automated1 > test_msas/automated1/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -nogaps > test_msas/nogaps/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -noallgaps > test_msas/noallgaps/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -gappyout > test_msas/gappyout/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -strict > test_msas/strict/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -strictplus > test_msas/strictplus/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -automated1 > test_msas/automated1/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -nogaps > test_msas/nogaps/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -noallgaps > test_msas/noallgaps/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -gappyout > test_msas/gappyout/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -strict > test_msas/strict/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -strictplus > test_msas/strictplus/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -automated1 > test_msas/automated1/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -nogaps > test_msas/nogaps/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -noallgaps > test_msas/noallgaps/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -gappyout > test_msas/gappyout/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strict > test_msas/strict/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strictplus > test_msas/strictplus/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -automated1 > test_msas/automated1/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -nogaps > test_msas/nogaps/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -noallgaps > test_msas/noallgaps/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -gappyout > test_msas/gappyout/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strict > test_msas/strict/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strictplus > test_msas/strictplus/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -automated1 > test_msas/automated1/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -nogaps > test_msas/nogaps/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -noallgaps > test_msas/noallgaps/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -gappyout > test_msas/gappyout/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -strict > test_msas/strict/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -strictplus > test_msas/strictplus/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -automated1 > test_msas/automated1/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -nogaps > test_msas/nogaps/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -noallgaps > test_msas/noallgaps/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -gappyout > test_msas/gappyout/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -strict > test_msas/strict/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -strictplus > test_msas/strictplus/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -automated1 > test_msas/automated1/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -nogaps > test_msas/nogaps/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -noallgaps > test_msas/noallgaps/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -gappyout > test_msas/gappyout/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -strict > test_msas/strict/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -strictplus > test_msas/strictplus/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -automated1 > test_msas/automated1/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -nogaps > test_msas/nogaps/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -noallgaps > test_msas/noallgaps/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -gappyout > test_msas/gappyout/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -strict > test_msas/strict/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -strictplus > test_msas/strictplus/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -automated1 > test_msas/automated1/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -nogaps > test_msas/nogaps/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -noallgaps > test_msas/noallgaps/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -gappyout > test_msas/gappyout/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -strict > test_msas/strict/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -strictplus > test_msas/strictplus/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -automated1 > test_msas/automated1/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -nogaps > test_msas/nogaps/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -noallgaps > test_msas/noallgaps/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -gappyout > test_msas/gappyout/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -strict > test_msas/strict/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -strictplus > test_msas/strictplus/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -automated1 > test_msas/automated1/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -nogaps > test_msas/nogaps/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -noallgaps > test_msas/noallgaps/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -gappyout > test_msas/gappyout/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -strict > test_msas/strict/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -strictplus > test_msas/strictplus/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -automated1 > test_msas/automated1/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -nogaps > test_msas/nogaps/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -noallgaps > test_msas/noallgaps/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -gappyout > test_msas/gappyout/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -strict > test_msas/strict/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -strictplus > test_msas/strictplus/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -automated1 > test_msas/automated1/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -nogaps > test_msas/nogaps/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -noallgaps > test_msas/noallgaps/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -gappyout > test_msas/gappyout/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -strict > test_msas/strict/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -strictplus > test_msas/strictplus/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -automated1 > test_msas/automated1/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -nogaps > test_msas/nogaps/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -noallgaps > test_msas/noallgaps/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -gappyout > test_msas/gappyout/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -strict > test_msas/strict/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -strictplus > test_msas/strictplus/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -automated1 > test_msas/automated1/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -nogaps > test_msas/nogaps/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -noallgaps > test_msas/noallgaps/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -gappyout > test_msas/gappyout/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -strict > test_msas/strict/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -strictplus > test_msas/strictplus/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -automated1 > test_msas/automated1/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -nogaps > test_msas/nogaps/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -noallgaps > test_msas/noallgaps/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -gappyout > test_msas/gappyout/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -strict > test_msas/strict/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -strictplus > test_msas/strictplus/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -automated1 > test_msas/automated1/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -nogaps > test_msas/nogaps/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -noallgaps > test_msas/noallgaps/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -gappyout > test_msas/gappyout/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -strict > test_msas/strict/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -strictplus > test_msas/strictplus/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -automated1 > test_msas/automated1/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -nogaps > test_msas/nogaps/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -noallgaps > test_msas/noallgaps/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -gappyout > test_msas/gappyout/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -strict > test_msas/strict/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -strictplus > test_msas/strictplus/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -automated1 > test_msas/automated1/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -nogaps > test_msas/nogaps/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -noallgaps > test_msas/noallgaps/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -gappyout > test_msas/gappyout/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -strict > test_msas/strict/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -strictplus > test_msas/strictplus/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -automated1 > test_msas/automated1/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -nogaps > test_msas/nogaps/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -noallgaps > test_msas/noallgaps/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -gappyout > test_msas/gappyout/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -strict > test_msas/strict/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -strictplus > test_msas/strictplus/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -automated1 > test_msas/automated1/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -nogaps > test_msas/nogaps/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -noallgaps > test_msas/noallgaps/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -gappyout > test_msas/gappyout/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -strict > test_msas/strict/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -strictplus > test_msas/strictplus/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -automated1 > test_msas/automated1/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -nogaps > test_msas/nogaps/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -noallgaps > test_msas/noallgaps/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -gappyout > test_msas/gappyout/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -strict > test_msas/strict/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -strictplus > test_msas/strictplus/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -automated1 > test_msas/automated1/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -nogaps > test_msas/nogaps/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -noallgaps > test_msas/noallgaps/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -gappyout > test_msas/gappyout/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -strict > test_msas/strict/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -strictplus > test_msas/strictplus/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -automated1 > test_msas/automated1/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -nogaps > test_msas/nogaps/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -noallgaps > test_msas/noallgaps/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -gappyout > test_msas/gappyout/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -strict > test_msas/strict/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -strictplus > test_msas/strictplus/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -automated1 > test_msas/automated1/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -nogaps > test_msas/nogaps/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -noallgaps > test_msas/noallgaps/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -gappyout > test_msas/gappyout/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -strict > test_msas/strict/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -strictplus > test_msas/strictplus/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -automated1 > test_msas/automated1/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -nogaps > test_msas/nogaps/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -noallgaps > test_msas/noallgaps/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -gappyout > test_msas/gappyout/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -strict > test_msas/strict/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -strictplus > test_msas/strictplus/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -automated1 > test_msas/automated1/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -nogaps > test_msas/nogaps/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -noallgaps > test_msas/noallgaps/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -gappyout > test_msas/gappyout/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -strict > test_msas/strict/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -strictplus > test_msas/strictplus/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -automated1 > test_msas/automated1/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -nogaps > test_msas/nogaps/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -noallgaps > test_msas/noallgaps/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -gappyout > test_msas/gappyout/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -strict > test_msas/strict/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -strictplus > test_msas/strictplus/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -automated1 > test_msas/automated1/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -nogaps > test_msas/nogaps/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -noallgaps > test_msas/noallgaps/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -gappyout > test_msas/gappyout/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -strict > test_msas/strict/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -strictplus > test_msas/strictplus/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -automated1 > test_msas/automated1/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -nogaps > test_msas/nogaps/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -noallgaps > test_msas/noallgaps/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -gappyout > test_msas/gappyout/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -strict > test_msas/strict/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -strictplus > test_msas/strictplus/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -automated1 > test_msas/automated1/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -nogaps > test_msas/nogaps/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -noallgaps > test_msas/noallgaps/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -gappyout > test_msas/gappyout/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -strict > test_msas/strict/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -strictplus > test_msas/strictplus/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -automated1 > test_msas/automated1/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -nogaps > test_msas/nogaps/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -noallgaps > test_msas/noallgaps/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -gappyout > test_msas/gappyout/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -strict > test_msas/strict/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -strictplus > test_msas/strictplus/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -automated1 > test_msas/automated1/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -nogaps > test_msas/nogaps/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -noallgaps > test_msas/noallgaps/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -gappyout > test_msas/gappyout/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -strict > test_msas/strict/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -strictplus > test_msas/strictplus/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -automated1 > test_msas/automated1/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -nogaps > test_msas/nogaps/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -noallgaps > test_msas/noallgaps/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -gappyout > test_msas/gappyout/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -strict > test_msas/strict/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -strictplus > test_msas/strictplus/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -automated1 > test_msas/automated1/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -nogaps > test_msas/nogaps/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -noallgaps > test_msas/noallgaps/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -gappyout > test_msas/gappyout/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -strict > test_msas/strict/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -strictplus > test_msas/strictplus/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -automated1 > test_msas/automated1/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -nogaps > test_msas/nogaps/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -noallgaps > test_msas/noallgaps/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -gappyout > test_msas/gappyout/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -strict > test_msas/strict/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -strictplus > test_msas/strictplus/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -automated1 > test_msas/automated1/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -nogaps > test_msas/nogaps/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -noallgaps > test_msas/noallgaps/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -gappyout > test_msas/gappyout/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -strict > test_msas/strict/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -strictplus > test_msas/strictplus/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -automated1 > test_msas/automated1/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -nogaps > test_msas/nogaps/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -noallgaps > test_msas/noallgaps/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -gappyout > test_msas/gappyout/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -strict > test_msas/strict/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -strictplus > test_msas/strictplus/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -automated1 > test_msas/automated1/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -nogaps > test_msas/nogaps/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -noallgaps > test_msas/noallgaps/example.091.AA.strNOG.ENOG411BWBU.fasta + From 940b1197da1404489e34090e5bdd435e3ecdd2cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 13:00:09 +0200 Subject: [PATCH 24/61] Consider empty files --- scripts/compare_trimmed_msas.ps1 | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/scripts/compare_trimmed_msas.ps1 b/scripts/compare_trimmed_msas.ps1 index b605c5e32..f47803348 100644 --- a/scripts/compare_trimmed_msas.ps1 +++ b/scripts/compare_trimmed_msas.ps1 @@ -19,7 +19,17 @@ foreach ($method in $methods) { exit 1 } - $result = Compare-Object (Get-Content $test_file) (Get-Content $reference_file) -SyncWindow 0 + $test_content = Get-Content $test_file + $reference_content = Get-Content $reference_file + + # Check if both files are empty + if ($test_content.Count -eq 0 -and $reference_content.Count -eq 0) { + Write-Output "Both $test_file and $reference_file are empty and considered equal." + continue + } + + # Compare contents + $result = Compare-Object $test_content $reference_content -SyncWindow 0 if ($result) { Write-Output "Files $test_file and $reference_file differ." exit 1 From 81b95b7fc2ae806594401b5b9789e351dfde8a4a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 10 Jul 2024 13:00:47 +0200 Subject: [PATCH 25/61] Recover old tests --- scripts/generate_trimmed_msas.sh | 499 ++++++++++++++++++++++++++++++- 1 file changed, 498 insertions(+), 1 deletion(-) diff --git a/scripts/generate_trimmed_msas.sh b/scripts/generate_trimmed_msas.sh index 5a04008a4..fcc05d90e 100755 --- a/scripts/generate_trimmed_msas.sh +++ b/scripts/generate_trimmed_msas.sh @@ -12,4 +12,501 @@ mkdir test_msas/noallgaps ./source/trimal -in dataset/example.004.AA.fasta -automated1 > test_msas/automated1/example.004.AA.fasta ./source/trimal -in dataset/example.004.AA.fasta -nogaps > test_msas/nogaps/example.004.AA.fasta ./source/trimal -in dataset/example.004.AA.fasta -noallgaps > test_msas/noallgaps/example.004.AA.fasta - +./source/trimal -in dataset/example.005.AA.fasta -gappyout > test_msas/gappyout/example.005.AA.fasta +./source/trimal -in dataset/example.005.AA.fasta -strict > test_msas/strict/example.005.AA.fasta +./source/trimal -in dataset/example.005.AA.fasta -strictplus > test_msas/strictplus/example.005.AA.fasta +./source/trimal -in dataset/example.005.AA.fasta -automated1 > test_msas/automated1/example.005.AA.fasta +./source/trimal -in dataset/example.005.AA.fasta -nogaps > test_msas/nogaps/example.005.AA.fasta +./source/trimal -in dataset/example.005.AA.fasta -noallgaps > test_msas/noallgaps/example.005.AA.fasta +./source/trimal -in dataset/example.007.AA.fasta -gappyout > test_msas/gappyout/example.007.AA.fasta +./source/trimal -in dataset/example.007.AA.fasta -strict > test_msas/strict/example.007.AA.fasta +./source/trimal -in dataset/example.007.AA.fasta -strictplus > test_msas/strictplus/example.007.AA.fasta +./source/trimal -in dataset/example.007.AA.fasta -automated1 > test_msas/automated1/example.007.AA.fasta +./source/trimal -in dataset/example.007.AA.fasta -nogaps > test_msas/nogaps/example.007.AA.fasta +./source/trimal -in dataset/example.007.AA.fasta -noallgaps > test_msas/noallgaps/example.007.AA.fasta +./source/trimal -in dataset/example.009.AA.fasta -gappyout > test_msas/gappyout/example.009.AA.fasta +./source/trimal -in dataset/example.009.AA.fasta -strict > test_msas/strict/example.009.AA.fasta +./source/trimal -in dataset/example.009.AA.fasta -strictplus > test_msas/strictplus/example.009.AA.fasta +./source/trimal -in dataset/example.009.AA.fasta -automated1 > test_msas/automated1/example.009.AA.fasta +./source/trimal -in dataset/example.009.AA.fasta -nogaps > test_msas/nogaps/example.009.AA.fasta +./source/trimal -in dataset/example.009.AA.fasta -noallgaps > test_msas/noallgaps/example.009.AA.fasta +./source/trimal -in dataset/example.010.AA.fasta -gappyout > test_msas/gappyout/example.010.AA.fasta +./source/trimal -in dataset/example.010.AA.fasta -strict > test_msas/strict/example.010.AA.fasta +./source/trimal -in dataset/example.010.AA.fasta -strictplus > test_msas/strictplus/example.010.AA.fasta +./source/trimal -in dataset/example.010.AA.fasta -automated1 > test_msas/automated1/example.010.AA.fasta +./source/trimal -in dataset/example.010.AA.fasta -nogaps > test_msas/nogaps/example.010.AA.fasta +./source/trimal -in dataset/example.010.AA.fasta -noallgaps > test_msas/noallgaps/example.010.AA.fasta +./source/trimal -in dataset/example.011.AA.YKL197C.fasta -gappyout > test_msas/gappyout/example.011.AA.YKL197C.fasta +./source/trimal -in dataset/example.011.AA.YKL197C.fasta -strict > test_msas/strict/example.011.AA.YKL197C.fasta +./source/trimal -in dataset/example.011.AA.YKL197C.fasta -strictplus > test_msas/strictplus/example.011.AA.YKL197C.fasta +./source/trimal -in dataset/example.011.AA.YKL197C.fasta -automated1 > test_msas/automated1/example.011.AA.YKL197C.fasta +./source/trimal -in dataset/example.011.AA.YKL197C.fasta -nogaps > test_msas/nogaps/example.011.AA.YKL197C.fasta +./source/trimal -in dataset/example.011.AA.YKL197C.fasta -noallgaps > test_msas/noallgaps/example.011.AA.YKL197C.fasta +./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -gappyout > test_msas/gappyout/example.014.AA.EggNOG.COG0591.fasta +./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -strict > test_msas/strict/example.014.AA.EggNOG.COG0591.fasta +./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -strictplus > test_msas/strictplus/example.014.AA.EggNOG.COG0591.fasta +./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -automated1 > test_msas/automated1/example.014.AA.EggNOG.COG0591.fasta +./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -nogaps > test_msas/nogaps/example.014.AA.EggNOG.COG0591.fasta +./source/trimal -in dataset/example.014.AA.EggNOG.COG0591.fasta -noallgaps > test_msas/noallgaps/example.014.AA.EggNOG.COG0591.fasta +./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -gappyout > test_msas/gappyout/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -strict > test_msas/strict/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -strictplus > test_msas/strictplus/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -automated1 > test_msas/automated1/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -nogaps > test_msas/nogaps/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -noallgaps > test_msas/noallgaps/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -gappyout > test_msas/gappyout/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -strict > test_msas/strict/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -strictplus > test_msas/strictplus/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -automated1 > test_msas/automated1/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -nogaps > test_msas/nogaps/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -noallgaps > test_msas/noallgaps/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -gappyout > test_msas/gappyout/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -strict > test_msas/strict/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -strictplus > test_msas/strictplus/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -automated1 > test_msas/automated1/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -nogaps > test_msas/nogaps/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -noallgaps > test_msas/noallgaps/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -gappyout > test_msas/gappyout/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -strict > test_msas/strict/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -strictplus > test_msas/strictplus/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -automated1 > test_msas/automated1/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -nogaps > test_msas/nogaps/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -noallgaps > test_msas/noallgaps/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -gappyout > test_msas/gappyout/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -strict > test_msas/strict/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -strictplus > test_msas/strictplus/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -automated1 > test_msas/automated1/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -nogaps > test_msas/nogaps/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -noallgaps > test_msas/noallgaps/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -gappyout > test_msas/gappyout/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -strict > test_msas/strict/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -strictplus > test_msas/strictplus/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -automated1 > test_msas/automated1/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -nogaps > test_msas/nogaps/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -noallgaps > test_msas/noallgaps/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -gappyout > test_msas/gappyout/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -strict > test_msas/strict/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -strictplus > test_msas/strictplus/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -automated1 > test_msas/automated1/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -nogaps > test_msas/nogaps/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -noallgaps > test_msas/noallgaps/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -gappyout > test_msas/gappyout/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -strict > test_msas/strict/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -strictplus > test_msas/strictplus/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -automated1 > test_msas/automated1/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -nogaps > test_msas/nogaps/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -noallgaps > test_msas/noallgaps/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -gappyout > test_msas/gappyout/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -strict > test_msas/strict/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -strictplus > test_msas/strictplus/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -automated1 > test_msas/automated1/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -nogaps > test_msas/nogaps/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -noallgaps > test_msas/noallgaps/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -gappyout > test_msas/gappyout/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -strict > test_msas/strict/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -strictplus > test_msas/strictplus/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -automated1 > test_msas/automated1/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -nogaps > test_msas/nogaps/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -noallgaps > test_msas/noallgaps/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -gappyout > test_msas/gappyout/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -strict > test_msas/strict/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -strictplus > test_msas/strictplus/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -automated1 > test_msas/automated1/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -nogaps > test_msas/nogaps/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -noallgaps > test_msas/noallgaps/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -gappyout > test_msas/gappyout/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -strict > test_msas/strict/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -strictplus > test_msas/strictplus/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -automated1 > test_msas/automated1/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -nogaps > test_msas/nogaps/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -noallgaps > test_msas/noallgaps/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -gappyout > test_msas/gappyout/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -strict > test_msas/strict/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -strictplus > test_msas/strictplus/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -automated1 > test_msas/automated1/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -nogaps > test_msas/nogaps/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -noallgaps > test_msas/noallgaps/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -gappyout > test_msas/gappyout/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -strict > test_msas/strict/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -strictplus > test_msas/strictplus/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -automated1 > test_msas/automated1/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -nogaps > test_msas/nogaps/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -noallgaps > test_msas/noallgaps/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -gappyout > test_msas/gappyout/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -strict > test_msas/strict/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -strictplus > test_msas/strictplus/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -automated1 > test_msas/automated1/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -nogaps > test_msas/nogaps/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -noallgaps > test_msas/noallgaps/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -gappyout > test_msas/gappyout/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -strict > test_msas/strict/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -strictplus > test_msas/strictplus/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -automated1 > test_msas/automated1/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -nogaps > test_msas/nogaps/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -noallgaps > test_msas/noallgaps/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -gappyout > test_msas/gappyout/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -strict > test_msas/strict/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -strictplus > test_msas/strictplus/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -automated1 > test_msas/automated1/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -nogaps > test_msas/nogaps/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -noallgaps > test_msas/noallgaps/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -gappyout > test_msas/gappyout/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -strict > test_msas/strict/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -strictplus > test_msas/strictplus/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -automated1 > test_msas/automated1/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -nogaps > test_msas/nogaps/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -noallgaps > test_msas/noallgaps/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -gappyout > test_msas/gappyout/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -strict > test_msas/strict/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -strictplus > test_msas/strictplus/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -automated1 > test_msas/automated1/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -nogaps > test_msas/nogaps/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -noallgaps > test_msas/noallgaps/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -gappyout > test_msas/gappyout/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -strict > test_msas/strict/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -strictplus > test_msas/strictplus/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -automated1 > test_msas/automated1/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -nogaps > test_msas/nogaps/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -noallgaps > test_msas/noallgaps/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -gappyout > test_msas/gappyout/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -strict > test_msas/strict/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -strictplus > test_msas/strictplus/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -automated1 > test_msas/automated1/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -nogaps > test_msas/nogaps/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -noallgaps > test_msas/noallgaps/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -gappyout > test_msas/gappyout/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -strict > test_msas/strict/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -strictplus > test_msas/strictplus/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -automated1 > test_msas/automated1/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -nogaps > test_msas/nogaps/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -noallgaps > test_msas/noallgaps/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -gappyout > test_msas/gappyout/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -strict > test_msas/strict/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -strictplus > test_msas/strictplus/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -automated1 > test_msas/automated1/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -nogaps > test_msas/nogaps/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -noallgaps > test_msas/noallgaps/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -gappyout > test_msas/gappyout/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -strict > test_msas/strict/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -strictplus > test_msas/strictplus/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -automated1 > test_msas/automated1/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -nogaps > test_msas/nogaps/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -noallgaps > test_msas/noallgaps/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -gappyout > test_msas/gappyout/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -strict > test_msas/strict/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -strictplus > test_msas/strictplus/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -automated1 > test_msas/automated1/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -nogaps > test_msas/nogaps/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -noallgaps > test_msas/noallgaps/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -gappyout > test_msas/gappyout/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -strict > test_msas/strict/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -strictplus > test_msas/strictplus/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -automated1 > test_msas/automated1/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -nogaps > test_msas/nogaps/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -noallgaps > test_msas/noallgaps/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -gappyout > test_msas/gappyout/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -strict > test_msas/strict/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -strictplus > test_msas/strictplus/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -automated1 > test_msas/automated1/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -nogaps > test_msas/nogaps/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -noallgaps > test_msas/noallgaps/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -gappyout > test_msas/gappyout/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -strict > test_msas/strict/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -strictplus > test_msas/strictplus/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -automated1 > test_msas/automated1/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -nogaps > test_msas/nogaps/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -noallgaps > test_msas/noallgaps/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -gappyout > test_msas/gappyout/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -strict > test_msas/strict/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -strictplus > test_msas/strictplus/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -automated1 > test_msas/automated1/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -nogaps > test_msas/nogaps/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -noallgaps > test_msas/noallgaps/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -gappyout > test_msas/gappyout/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -strict > test_msas/strict/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -strictplus > test_msas/strictplus/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -automated1 > test_msas/automated1/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -nogaps > test_msas/nogaps/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -noallgaps > test_msas/noallgaps/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -gappyout > test_msas/gappyout/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -strict > test_msas/strict/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -strictplus > test_msas/strictplus/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -automated1 > test_msas/automated1/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -nogaps > test_msas/nogaps/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -noallgaps > test_msas/noallgaps/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -gappyout > test_msas/gappyout/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -strict > test_msas/strict/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -strictplus > test_msas/strictplus/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -automated1 > test_msas/automated1/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -nogaps > test_msas/nogaps/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -noallgaps > test_msas/noallgaps/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -gappyout > test_msas/gappyout/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -strict > test_msas/strict/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -strictplus > test_msas/strictplus/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -automated1 > test_msas/automated1/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -nogaps > test_msas/nogaps/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -noallgaps > test_msas/noallgaps/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -gappyout > test_msas/gappyout/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strict > test_msas/strict/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strictplus > test_msas/strictplus/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -automated1 > test_msas/automated1/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -nogaps > test_msas/nogaps/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -noallgaps > test_msas/noallgaps/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -gappyout > test_msas/gappyout/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -strict > test_msas/strict/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -strictplus > test_msas/strictplus/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -automated1 > test_msas/automated1/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -nogaps > test_msas/nogaps/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -noallgaps > test_msas/noallgaps/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -gappyout > test_msas/gappyout/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strict > test_msas/strict/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strictplus > test_msas/strictplus/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -automated1 > test_msas/automated1/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -nogaps > test_msas/nogaps/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -noallgaps > test_msas/noallgaps/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -gappyout > test_msas/gappyout/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strict > test_msas/strict/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strictplus > test_msas/strictplus/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -automated1 > test_msas/automated1/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -nogaps > test_msas/nogaps/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -noallgaps > test_msas/noallgaps/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -gappyout > test_msas/gappyout/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -strict > test_msas/strict/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -strictplus > test_msas/strictplus/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -automated1 > test_msas/automated1/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -nogaps > test_msas/nogaps/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -noallgaps > test_msas/noallgaps/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -gappyout > test_msas/gappyout/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -strict > test_msas/strict/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -strictplus > test_msas/strictplus/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -automated1 > test_msas/automated1/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -nogaps > test_msas/nogaps/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -noallgaps > test_msas/noallgaps/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -gappyout > test_msas/gappyout/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -strict > test_msas/strict/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -strictplus > test_msas/strictplus/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -automated1 > test_msas/automated1/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -nogaps > test_msas/nogaps/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -noallgaps > test_msas/noallgaps/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -gappyout > test_msas/gappyout/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -strict > test_msas/strict/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -strictplus > test_msas/strictplus/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -automated1 > test_msas/automated1/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -nogaps > test_msas/nogaps/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -noallgaps > test_msas/noallgaps/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -gappyout > test_msas/gappyout/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strict > test_msas/strict/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strictplus > test_msas/strictplus/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -automated1 > test_msas/automated1/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -nogaps > test_msas/nogaps/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -noallgaps > test_msas/noallgaps/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -gappyout > test_msas/gappyout/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strict > test_msas/strict/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strictplus > test_msas/strictplus/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -automated1 > test_msas/automated1/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -nogaps > test_msas/nogaps/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -noallgaps > test_msas/noallgaps/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -gappyout > test_msas/gappyout/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -strict > test_msas/strict/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -strictplus > test_msas/strictplus/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -automated1 > test_msas/automated1/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -nogaps > test_msas/nogaps/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -noallgaps > test_msas/noallgaps/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -gappyout > test_msas/gappyout/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -strict > test_msas/strict/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -strictplus > test_msas/strictplus/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -automated1 > test_msas/automated1/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -nogaps > test_msas/nogaps/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -noallgaps > test_msas/noallgaps/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -gappyout > test_msas/gappyout/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -strict > test_msas/strict/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -strictplus > test_msas/strictplus/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -automated1 > test_msas/automated1/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -nogaps > test_msas/nogaps/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -noallgaps > test_msas/noallgaps/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -gappyout > test_msas/gappyout/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -strict > test_msas/strict/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -strictplus > test_msas/strictplus/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -automated1 > test_msas/automated1/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -nogaps > test_msas/nogaps/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -noallgaps > test_msas/noallgaps/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -gappyout > test_msas/gappyout/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -strict > test_msas/strict/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -strictplus > test_msas/strictplus/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -automated1 > test_msas/automated1/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -nogaps > test_msas/nogaps/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -noallgaps > test_msas/noallgaps/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -gappyout > test_msas/gappyout/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -strict > test_msas/strict/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -strictplus > test_msas/strictplus/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -automated1 > test_msas/automated1/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -nogaps > test_msas/nogaps/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -noallgaps > test_msas/noallgaps/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -gappyout > test_msas/gappyout/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -strict > test_msas/strict/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -strictplus > test_msas/strictplus/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -automated1 > test_msas/automated1/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -nogaps > test_msas/nogaps/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -noallgaps > test_msas/noallgaps/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -gappyout > test_msas/gappyout/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -strict > test_msas/strict/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -strictplus > test_msas/strictplus/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -automated1 > test_msas/automated1/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -nogaps > test_msas/nogaps/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -noallgaps > test_msas/noallgaps/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -gappyout > test_msas/gappyout/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -strict > test_msas/strict/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -strictplus > test_msas/strictplus/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -automated1 > test_msas/automated1/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -nogaps > test_msas/nogaps/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -noallgaps > test_msas/noallgaps/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -gappyout > test_msas/gappyout/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -strict > test_msas/strict/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -strictplus > test_msas/strictplus/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -automated1 > test_msas/automated1/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -nogaps > test_msas/nogaps/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -noallgaps > test_msas/noallgaps/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -gappyout > test_msas/gappyout/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -strict > test_msas/strict/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -strictplus > test_msas/strictplus/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -automated1 > test_msas/automated1/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -nogaps > test_msas/nogaps/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -noallgaps > test_msas/noallgaps/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -gappyout > test_msas/gappyout/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -strict > test_msas/strict/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -strictplus > test_msas/strictplus/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -automated1 > test_msas/automated1/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -nogaps > test_msas/nogaps/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -noallgaps > test_msas/noallgaps/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -gappyout > test_msas/gappyout/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -strict > test_msas/strict/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -strictplus > test_msas/strictplus/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -automated1 > test_msas/automated1/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -nogaps > test_msas/nogaps/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -noallgaps > test_msas/noallgaps/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -gappyout > test_msas/gappyout/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -strict > test_msas/strict/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -strictplus > test_msas/strictplus/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -automated1 > test_msas/automated1/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -nogaps > test_msas/nogaps/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -noallgaps > test_msas/noallgaps/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -gappyout > test_msas/gappyout/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -strict > test_msas/strict/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -strictplus > test_msas/strictplus/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -automated1 > test_msas/automated1/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -nogaps > test_msas/nogaps/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -noallgaps > test_msas/noallgaps/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -gappyout > test_msas/gappyout/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -strict > test_msas/strict/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -strictplus > test_msas/strictplus/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -automated1 > test_msas/automated1/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -nogaps > test_msas/nogaps/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -noallgaps > test_msas/noallgaps/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -gappyout > test_msas/gappyout/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -strict > test_msas/strict/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -strictplus > test_msas/strictplus/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -automated1 > test_msas/automated1/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -nogaps > test_msas/nogaps/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -noallgaps > test_msas/noallgaps/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -gappyout > test_msas/gappyout/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -strict > test_msas/strict/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -strictplus > test_msas/strictplus/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -automated1 > test_msas/automated1/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -nogaps > test_msas/nogaps/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -noallgaps > test_msas/noallgaps/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -gappyout > test_msas/gappyout/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -strict > test_msas/strict/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -strictplus > test_msas/strictplus/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -automated1 > test_msas/automated1/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -nogaps > test_msas/nogaps/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -noallgaps > test_msas/noallgaps/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -gappyout > test_msas/gappyout/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -strict > test_msas/strict/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -strictplus > test_msas/strictplus/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -automated1 > test_msas/automated1/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -nogaps > test_msas/nogaps/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -noallgaps > test_msas/noallgaps/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -gappyout > test_msas/gappyout/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -strict > test_msas/strict/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -strictplus > test_msas/strictplus/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -automated1 > test_msas/automated1/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -nogaps > test_msas/nogaps/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -noallgaps > test_msas/noallgaps/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -gappyout > test_msas/gappyout/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -strict > test_msas/strict/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -strictplus > test_msas/strictplus/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -automated1 > test_msas/automated1/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -nogaps > test_msas/nogaps/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -noallgaps > test_msas/noallgaps/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -gappyout > test_msas/gappyout/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -strict > test_msas/strict/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -strictplus > test_msas/strictplus/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -automated1 > test_msas/automated1/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -nogaps > test_msas/nogaps/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -noallgaps > test_msas/noallgaps/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -gappyout > test_msas/gappyout/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -strict > test_msas/strict/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -strictplus > test_msas/strictplus/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -automated1 > test_msas/automated1/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -nogaps > test_msas/nogaps/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -noallgaps > test_msas/noallgaps/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -gappyout > test_msas/gappyout/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -strict > test_msas/strict/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -strictplus > test_msas/strictplus/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -automated1 > test_msas/automated1/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -nogaps > test_msas/nogaps/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -noallgaps > test_msas/noallgaps/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -gappyout > test_msas/gappyout/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -strict > test_msas/strict/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -strictplus > test_msas/strictplus/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -automated1 > test_msas/automated1/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -nogaps > test_msas/nogaps/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -noallgaps > test_msas/noallgaps/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -gappyout > test_msas/gappyout/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -strict > test_msas/strict/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -strictplus > test_msas/strictplus/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -automated1 > test_msas/automated1/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -nogaps > test_msas/nogaps/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -noallgaps > test_msas/noallgaps/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -gappyout > test_msas/gappyout/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -strict > test_msas/strict/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -strictplus > test_msas/strictplus/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -automated1 > test_msas/automated1/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -nogaps > test_msas/nogaps/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -noallgaps > test_msas/noallgaps/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -gappyout > test_msas/gappyout/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -strict > test_msas/strict/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -strictplus > test_msas/strictplus/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -automated1 > test_msas/automated1/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -nogaps > test_msas/nogaps/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -noallgaps > test_msas/noallgaps/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -gappyout > test_msas/gappyout/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -strict > test_msas/strict/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -strictplus > test_msas/strictplus/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -automated1 > test_msas/automated1/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -nogaps > test_msas/nogaps/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -noallgaps > test_msas/noallgaps/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -gappyout > test_msas/gappyout/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -strict > test_msas/strict/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -strictplus > test_msas/strictplus/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -automated1 > test_msas/automated1/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -nogaps > test_msas/nogaps/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -noallgaps > test_msas/noallgaps/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -gappyout > test_msas/gappyout/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -strict > test_msas/strict/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -strictplus > test_msas/strictplus/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -automated1 > test_msas/automated1/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -nogaps > test_msas/nogaps/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -noallgaps > test_msas/noallgaps/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -gappyout > test_msas/gappyout/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -strict > test_msas/strict/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -strictplus > test_msas/strictplus/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -automated1 > test_msas/automated1/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -nogaps > test_msas/nogaps/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -noallgaps > test_msas/noallgaps/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -gappyout > test_msas/gappyout/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -strict > test_msas/strict/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -strictplus > test_msas/strictplus/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -automated1 > test_msas/automated1/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -nogaps > test_msas/nogaps/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -noallgaps > test_msas/noallgaps/example.091.AA.strNOG.ENOG411BWBU.fasta From 35047b29a9afc3d69731f65327fd9340e168ce32 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Fri, 9 Aug 2024 14:27:58 +0200 Subject: [PATCH 26/61] Add Windows compilation tests --- .github/workflows/build.yml | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index a5ec9246c..94752f389 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -13,7 +13,7 @@ on: name: Build jobs: - build_and_test_windows: + download_and_test_windows: runs-on: windows-2022 steps: - uses: actions/checkout@v4 @@ -40,3 +40,26 @@ jobs: - name: Run compare_trimmed_msas.ps1 run: | powershell -ExecutionPolicy Bypass -File .\scripts\compare_trimmed_msas.ps1 + build_and_test_windows: + runs-on: windows-2022 + steps: + - uses: actions/checkout@v3 + - name: Set up MSYS2 + uses: msys2/setup-msys2@v2 + with: + msystem: MINGW64 + update: true + install: >- + make + mingw-w64-x86_64-gcc + file + - name: Build trimal for Windows x86_64 + run: | + cd source + make -f makefile.Windows + file trimal.exe + file readal.exe + file statal.exe + cd .. + ./scripts/generate_trimmed_msas.sh + ./scripts/compare_trimmed_msas.sh From 21144efd058111ef0be7b82870b2ff19db5a0608 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Fri, 9 Aug 2024 14:28:45 +0200 Subject: [PATCH 27/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 30096e3de..1f9a8f15a 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched +Temporary file to force Github Actions workflow to be launched. From 801b829b531353c9ba33bc809a7f1a3a65149537 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Fri, 9 Aug 2024 14:33:59 +0200 Subject: [PATCH 28/61] Change script lines to execute them --- .github/workflows/build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 94752f389..3f52c39d9 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -61,5 +61,5 @@ jobs: file readal.exe file statal.exe cd .. - ./scripts/generate_trimmed_msas.sh - ./scripts/compare_trimmed_msas.sh + bash scripts/generate_trimmed_msas.sh + bash scripts/compare_trimmed_msas.sh From e11f24d477efd84ce16eac863fbadc23b1bbeaf0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Fri, 9 Aug 2024 14:34:24 +0200 Subject: [PATCH 29/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 1f9a8f15a..30096e3de 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched. +Temporary file to force Github Actions workflow to be launched From 0350dcd912427a24b5e152456055f4b7dc3cc647 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Fri, 9 Aug 2024 14:41:28 +0200 Subject: [PATCH 30/61] Debug Windows tests --- .github/workflows/build.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 3f52c39d9..4c45ddc47 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -62,4 +62,6 @@ jobs: file statal.exe cd .. bash scripts/generate_trimmed_msas.sh + cat test_msas/gappyout/example.004.AA.fasta + cat dataset/trimmed_msas/gappyout/example.004.AA.fasta bash scripts/compare_trimmed_msas.sh From cb79b3fa3bb2bfff5b084cd9ff32a42cb729f5f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Fri, 9 Aug 2024 14:41:40 +0200 Subject: [PATCH 31/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 30096e3de..1f9a8f15a 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched +Temporary file to force Github Actions workflow to be launched. From 40416baf2cb72a68c824e5f1fb7ec9dc4334d3e0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Fri, 9 Aug 2024 14:46:56 +0200 Subject: [PATCH 32/61] Debug Windows tests --- .github/workflows/build.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 4c45ddc47..15aa8cba1 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -62,6 +62,8 @@ jobs: file statal.exe cd .. bash scripts/generate_trimmed_msas.sh + echo "test_msas/gappyout/example.004.AA.fasta" cat test_msas/gappyout/example.004.AA.fasta + echo "dataset/trimmed_msas/gappyout/example.004.AA.fasta" cat dataset/trimmed_msas/gappyout/example.004.AA.fasta bash scripts/compare_trimmed_msas.sh From 2270a2a48d3a1ce59b3702de3ad73d33f3568cf6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Fri, 9 Aug 2024 14:47:11 +0200 Subject: [PATCH 33/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 1f9a8f15a..30096e3de 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched. +Temporary file to force Github Actions workflow to be launched From cabf5fc1eced9c38f0b69d99e1ca0ed5a91bea4f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Fri, 9 Aug 2024 14:57:36 +0200 Subject: [PATCH 34/61] Add Windows script for testing --- scripts/generate_trimmed_msas_Windows.sh | 512 +++++++++++++++++++++++ 1 file changed, 512 insertions(+) create mode 100644 scripts/generate_trimmed_msas_Windows.sh diff --git a/scripts/generate_trimmed_msas_Windows.sh b/scripts/generate_trimmed_msas_Windows.sh new file mode 100644 index 000000000..cba5b3ed2 --- /dev/null +++ b/scripts/generate_trimmed_msas_Windows.sh @@ -0,0 +1,512 @@ +mkdir test_msas +mkdir test_msas/gappyout +mkdir test_msas/strict +mkdir test_msas/strictplus +mkdir test_msas/automated1 +mkdir test_msas/nogaps +mkdir test_msas/noallgaps + +./source/trimal.exe -in dataset/example.004.AA.fasta -gappyout > test_msas/gappyout/example.004.AA.fasta +./source/trimal.exe -in dataset/example.004.AA.fasta -strict > test_msas/strict/example.004.AA.fasta +./source/trimal.exe -in dataset/example.004.AA.fasta -strictplus > test_msas/strictplus/example.004.AA.fasta +./source/trimal.exe -in dataset/example.004.AA.fasta -automated1 > test_msas/automated1/example.004.AA.fasta +./source/trimal.exe -in dataset/example.004.AA.fasta -nogaps > test_msas/nogaps/example.004.AA.fasta +./source/trimal.exe -in dataset/example.004.AA.fasta -noallgaps > test_msas/noallgaps/example.004.AA.fasta +./source/trimal.exe -in dataset/example.005.AA.fasta -gappyout > test_msas/gappyout/example.005.AA.fasta +./source/trimal.exe -in dataset/example.005.AA.fasta -strict > test_msas/strict/example.005.AA.fasta +./source/trimal.exe -in dataset/example.005.AA.fasta -strictplus > test_msas/strictplus/example.005.AA.fasta +./source/trimal.exe -in dataset/example.005.AA.fasta -automated1 > test_msas/automated1/example.005.AA.fasta +./source/trimal.exe -in dataset/example.005.AA.fasta -nogaps > test_msas/nogaps/example.005.AA.fasta +./source/trimal.exe -in dataset/example.005.AA.fasta -noallgaps > test_msas/noallgaps/example.005.AA.fasta +./source/trimal.exe -in dataset/example.007.AA.fasta -gappyout > test_msas/gappyout/example.007.AA.fasta +./source/trimal.exe -in dataset/example.007.AA.fasta -strict > test_msas/strict/example.007.AA.fasta +./source/trimal.exe -in dataset/example.007.AA.fasta -strictplus > test_msas/strictplus/example.007.AA.fasta +./source/trimal.exe -in dataset/example.007.AA.fasta -automated1 > test_msas/automated1/example.007.AA.fasta +./source/trimal.exe -in dataset/example.007.AA.fasta -nogaps > test_msas/nogaps/example.007.AA.fasta +./source/trimal.exe -in dataset/example.007.AA.fasta -noallgaps > test_msas/noallgaps/example.007.AA.fasta +./source/trimal.exe -in dataset/example.009.AA.fasta -gappyout > test_msas/gappyout/example.009.AA.fasta +./source/trimal.exe -in dataset/example.009.AA.fasta -strict > test_msas/strict/example.009.AA.fasta +./source/trimal.exe -in dataset/example.009.AA.fasta -strictplus > test_msas/strictplus/example.009.AA.fasta +./source/trimal.exe -in dataset/example.009.AA.fasta -automated1 > test_msas/automated1/example.009.AA.fasta +./source/trimal.exe -in dataset/example.009.AA.fasta -nogaps > test_msas/nogaps/example.009.AA.fasta +./source/trimal.exe -in dataset/example.009.AA.fasta -noallgaps > test_msas/noallgaps/example.009.AA.fasta +./source/trimal.exe -in dataset/example.010.AA.fasta -gappyout > test_msas/gappyout/example.010.AA.fasta +./source/trimal.exe -in dataset/example.010.AA.fasta -strict > test_msas/strict/example.010.AA.fasta +./source/trimal.exe -in dataset/example.010.AA.fasta -strictplus > test_msas/strictplus/example.010.AA.fasta +./source/trimal.exe -in dataset/example.010.AA.fasta -automated1 > test_msas/automated1/example.010.AA.fasta +./source/trimal.exe -in dataset/example.010.AA.fasta -nogaps > test_msas/nogaps/example.010.AA.fasta +./source/trimal.exe -in dataset/example.010.AA.fasta -noallgaps > test_msas/noallgaps/example.010.AA.fasta +./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -gappyout > test_msas/gappyout/example.011.AA.YKL197C.fasta +./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -strict > test_msas/strict/example.011.AA.YKL197C.fasta +./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -strictplus > test_msas/strictplus/example.011.AA.YKL197C.fasta +./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -automated1 > test_msas/automated1/example.011.AA.YKL197C.fasta +./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -nogaps > test_msas/nogaps/example.011.AA.YKL197C.fasta +./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -noallgaps > test_msas/noallgaps/example.011.AA.YKL197C.fasta +./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -gappyout > test_msas/gappyout/example.014.AA.EggNOG.COG0591.fasta +./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -strict > test_msas/strict/example.014.AA.EggNOG.COG0591.fasta +./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -strictplus > test_msas/strictplus/example.014.AA.EggNOG.COG0591.fasta +./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -automated1 > test_msas/automated1/example.014.AA.EggNOG.COG0591.fasta +./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -nogaps > test_msas/nogaps/example.014.AA.EggNOG.COG0591.fasta +./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -noallgaps > test_msas/noallgaps/example.014.AA.EggNOG.COG0591.fasta +./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -gappyout > test_msas/gappyout/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -strict > test_msas/strict/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -strictplus > test_msas/strictplus/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -automated1 > test_msas/automated1/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -nogaps > test_msas/nogaps/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -noallgaps > test_msas/noallgaps/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -gappyout > test_msas/gappyout/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -strict > test_msas/strict/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -strictplus > test_msas/strictplus/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -automated1 > test_msas/automated1/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -nogaps > test_msas/nogaps/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -noallgaps > test_msas/noallgaps/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -gappyout > test_msas/gappyout/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -strict > test_msas/strict/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -strictplus > test_msas/strictplus/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -automated1 > test_msas/automated1/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -nogaps > test_msas/nogaps/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -noallgaps > test_msas/noallgaps/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -gappyout > test_msas/gappyout/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -strict > test_msas/strict/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -strictplus > test_msas/strictplus/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -automated1 > test_msas/automated1/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -nogaps > test_msas/nogaps/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -noallgaps > test_msas/noallgaps/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -gappyout > test_msas/gappyout/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -strict > test_msas/strict/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -strictplus > test_msas/strictplus/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -automated1 > test_msas/automated1/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -nogaps > test_msas/nogaps/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -noallgaps > test_msas/noallgaps/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -gappyout > test_msas/gappyout/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -strict > test_msas/strict/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -strictplus > test_msas/strictplus/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -automated1 > test_msas/automated1/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -nogaps > test_msas/nogaps/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -noallgaps > test_msas/noallgaps/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -gappyout > test_msas/gappyout/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -strict > test_msas/strict/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -strictplus > test_msas/strictplus/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -automated1 > test_msas/automated1/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -nogaps > test_msas/nogaps/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -noallgaps > test_msas/noallgaps/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -gappyout > test_msas/gappyout/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -strict > test_msas/strict/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -strictplus > test_msas/strictplus/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -automated1 > test_msas/automated1/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -nogaps > test_msas/nogaps/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -noallgaps > test_msas/noallgaps/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -gappyout > test_msas/gappyout/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -strict > test_msas/strict/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -strictplus > test_msas/strictplus/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -automated1 > test_msas/automated1/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -nogaps > test_msas/nogaps/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -noallgaps > test_msas/noallgaps/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -gappyout > test_msas/gappyout/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -strict > test_msas/strict/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -strictplus > test_msas/strictplus/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -automated1 > test_msas/automated1/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -nogaps > test_msas/nogaps/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -noallgaps > test_msas/noallgaps/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -gappyout > test_msas/gappyout/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -strict > test_msas/strict/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -strictplus > test_msas/strictplus/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -automated1 > test_msas/automated1/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -nogaps > test_msas/nogaps/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -noallgaps > test_msas/noallgaps/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -gappyout > test_msas/gappyout/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -strict > test_msas/strict/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -strictplus > test_msas/strictplus/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -automated1 > test_msas/automated1/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -nogaps > test_msas/nogaps/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -noallgaps > test_msas/noallgaps/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -gappyout > test_msas/gappyout/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -strict > test_msas/strict/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -strictplus > test_msas/strictplus/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -automated1 > test_msas/automated1/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -nogaps > test_msas/nogaps/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -noallgaps > test_msas/noallgaps/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -gappyout > test_msas/gappyout/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -strict > test_msas/strict/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -strictplus > test_msas/strictplus/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -automated1 > test_msas/automated1/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -nogaps > test_msas/nogaps/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -noallgaps > test_msas/noallgaps/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -gappyout > test_msas/gappyout/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -strict > test_msas/strict/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -strictplus > test_msas/strictplus/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -automated1 > test_msas/automated1/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -nogaps > test_msas/nogaps/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -noallgaps > test_msas/noallgaps/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -gappyout > test_msas/gappyout/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -strict > test_msas/strict/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -strictplus > test_msas/strictplus/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -automated1 > test_msas/automated1/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -nogaps > test_msas/nogaps/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -noallgaps > test_msas/noallgaps/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -gappyout > test_msas/gappyout/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -strict > test_msas/strict/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -strictplus > test_msas/strictplus/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -automated1 > test_msas/automated1/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -nogaps > test_msas/nogaps/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -noallgaps > test_msas/noallgaps/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -gappyout > test_msas/gappyout/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -strict > test_msas/strict/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -strictplus > test_msas/strictplus/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -automated1 > test_msas/automated1/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -nogaps > test_msas/nogaps/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -noallgaps > test_msas/noallgaps/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -gappyout > test_msas/gappyout/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -strict > test_msas/strict/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -strictplus > test_msas/strictplus/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -automated1 > test_msas/automated1/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -nogaps > test_msas/nogaps/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -noallgaps > test_msas/noallgaps/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -gappyout > test_msas/gappyout/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -strict > test_msas/strict/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -strictplus > test_msas/strictplus/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -automated1 > test_msas/automated1/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -nogaps > test_msas/nogaps/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -noallgaps > test_msas/noallgaps/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -gappyout > test_msas/gappyout/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -strict > test_msas/strict/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -strictplus > test_msas/strictplus/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -automated1 > test_msas/automated1/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -nogaps > test_msas/nogaps/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -noallgaps > test_msas/noallgaps/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -gappyout > test_msas/gappyout/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -strict > test_msas/strict/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -strictplus > test_msas/strictplus/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -automated1 > test_msas/automated1/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -nogaps > test_msas/nogaps/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -noallgaps > test_msas/noallgaps/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -gappyout > test_msas/gappyout/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -strict > test_msas/strict/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -strictplus > test_msas/strictplus/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -automated1 > test_msas/automated1/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -nogaps > test_msas/nogaps/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -noallgaps > test_msas/noallgaps/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -gappyout > test_msas/gappyout/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -strict > test_msas/strict/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -strictplus > test_msas/strictplus/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -automated1 > test_msas/automated1/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -nogaps > test_msas/nogaps/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -noallgaps > test_msas/noallgaps/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -gappyout > test_msas/gappyout/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -strict > test_msas/strict/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -strictplus > test_msas/strictplus/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -automated1 > test_msas/automated1/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -nogaps > test_msas/nogaps/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -noallgaps > test_msas/noallgaps/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -gappyout > test_msas/gappyout/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -strict > test_msas/strict/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -strictplus > test_msas/strictplus/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -automated1 > test_msas/automated1/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -nogaps > test_msas/nogaps/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -noallgaps > test_msas/noallgaps/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -gappyout > test_msas/gappyout/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -strict > test_msas/strict/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -strictplus > test_msas/strictplus/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -automated1 > test_msas/automated1/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -nogaps > test_msas/nogaps/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -noallgaps > test_msas/noallgaps/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -gappyout > test_msas/gappyout/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -strict > test_msas/strict/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -strictplus > test_msas/strictplus/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -automated1 > test_msas/automated1/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -nogaps > test_msas/nogaps/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -noallgaps > test_msas/noallgaps/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -gappyout > test_msas/gappyout/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -strict > test_msas/strict/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -strictplus > test_msas/strictplus/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -automated1 > test_msas/automated1/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -nogaps > test_msas/nogaps/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -noallgaps > test_msas/noallgaps/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -gappyout > test_msas/gappyout/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -strict > test_msas/strict/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -strictplus > test_msas/strictplus/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -automated1 > test_msas/automated1/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -nogaps > test_msas/nogaps/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -noallgaps > test_msas/noallgaps/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -gappyout > test_msas/gappyout/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -strict > test_msas/strict/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -strictplus > test_msas/strictplus/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -automated1 > test_msas/automated1/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -nogaps > test_msas/nogaps/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -noallgaps > test_msas/noallgaps/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -gappyout > test_msas/gappyout/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -strict > test_msas/strict/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -strictplus > test_msas/strictplus/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -automated1 > test_msas/automated1/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -nogaps > test_msas/nogaps/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -noallgaps > test_msas/noallgaps/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -gappyout > test_msas/gappyout/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -strict > test_msas/strict/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -strictplus > test_msas/strictplus/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -automated1 > test_msas/automated1/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -nogaps > test_msas/nogaps/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -noallgaps > test_msas/noallgaps/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -gappyout > test_msas/gappyout/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strict > test_msas/strict/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strictplus > test_msas/strictplus/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -automated1 > test_msas/automated1/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -nogaps > test_msas/nogaps/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -noallgaps > test_msas/noallgaps/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -gappyout > test_msas/gappyout/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -strict > test_msas/strict/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -strictplus > test_msas/strictplus/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -automated1 > test_msas/automated1/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -nogaps > test_msas/nogaps/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -noallgaps > test_msas/noallgaps/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -gappyout > test_msas/gappyout/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strict > test_msas/strict/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strictplus > test_msas/strictplus/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -automated1 > test_msas/automated1/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -nogaps > test_msas/nogaps/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -noallgaps > test_msas/noallgaps/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -gappyout > test_msas/gappyout/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strict > test_msas/strict/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strictplus > test_msas/strictplus/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -automated1 > test_msas/automated1/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -nogaps > test_msas/nogaps/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -noallgaps > test_msas/noallgaps/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -gappyout > test_msas/gappyout/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -strict > test_msas/strict/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -strictplus > test_msas/strictplus/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -automated1 > test_msas/automated1/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -nogaps > test_msas/nogaps/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -noallgaps > test_msas/noallgaps/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -gappyout > test_msas/gappyout/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -strict > test_msas/strict/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -strictplus > test_msas/strictplus/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -automated1 > test_msas/automated1/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -nogaps > test_msas/nogaps/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -noallgaps > test_msas/noallgaps/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -gappyout > test_msas/gappyout/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -strict > test_msas/strict/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -strictplus > test_msas/strictplus/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -automated1 > test_msas/automated1/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -nogaps > test_msas/nogaps/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -noallgaps > test_msas/noallgaps/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -gappyout > test_msas/gappyout/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -strict > test_msas/strict/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -strictplus > test_msas/strictplus/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -automated1 > test_msas/automated1/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -nogaps > test_msas/nogaps/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -noallgaps > test_msas/noallgaps/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -gappyout > test_msas/gappyout/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strict > test_msas/strict/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strictplus > test_msas/strictplus/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -automated1 > test_msas/automated1/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -nogaps > test_msas/nogaps/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -noallgaps > test_msas/noallgaps/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -gappyout > test_msas/gappyout/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strict > test_msas/strict/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strictplus > test_msas/strictplus/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -automated1 > test_msas/automated1/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -nogaps > test_msas/nogaps/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -noallgaps > test_msas/noallgaps/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -gappyout > test_msas/gappyout/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -strict > test_msas/strict/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -strictplus > test_msas/strictplus/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -automated1 > test_msas/automated1/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -nogaps > test_msas/nogaps/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -noallgaps > test_msas/noallgaps/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -gappyout > test_msas/gappyout/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -strict > test_msas/strict/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -strictplus > test_msas/strictplus/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -automated1 > test_msas/automated1/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -nogaps > test_msas/nogaps/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -noallgaps > test_msas/noallgaps/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -gappyout > test_msas/gappyout/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -strict > test_msas/strict/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -strictplus > test_msas/strictplus/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -automated1 > test_msas/automated1/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -nogaps > test_msas/nogaps/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -noallgaps > test_msas/noallgaps/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -gappyout > test_msas/gappyout/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -strict > test_msas/strict/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -strictplus > test_msas/strictplus/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -automated1 > test_msas/automated1/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -nogaps > test_msas/nogaps/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -noallgaps > test_msas/noallgaps/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -gappyout > test_msas/gappyout/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -strict > test_msas/strict/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -strictplus > test_msas/strictplus/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -automated1 > test_msas/automated1/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -nogaps > test_msas/nogaps/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -noallgaps > test_msas/noallgaps/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -gappyout > test_msas/gappyout/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -strict > test_msas/strict/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -strictplus > test_msas/strictplus/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -automated1 > test_msas/automated1/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -nogaps > test_msas/nogaps/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -noallgaps > test_msas/noallgaps/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -gappyout > test_msas/gappyout/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -strict > test_msas/strict/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -strictplus > test_msas/strictplus/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -automated1 > test_msas/automated1/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -nogaps > test_msas/nogaps/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -noallgaps > test_msas/noallgaps/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -gappyout > test_msas/gappyout/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -strict > test_msas/strict/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -strictplus > test_msas/strictplus/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -automated1 > test_msas/automated1/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -nogaps > test_msas/nogaps/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -noallgaps > test_msas/noallgaps/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -gappyout > test_msas/gappyout/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -strict > test_msas/strict/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -strictplus > test_msas/strictplus/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -automated1 > test_msas/automated1/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -nogaps > test_msas/nogaps/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -noallgaps > test_msas/noallgaps/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -gappyout > test_msas/gappyout/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -strict > test_msas/strict/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -strictplus > test_msas/strictplus/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -automated1 > test_msas/automated1/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -nogaps > test_msas/nogaps/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -noallgaps > test_msas/noallgaps/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -gappyout > test_msas/gappyout/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -strict > test_msas/strict/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -strictplus > test_msas/strictplus/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -automated1 > test_msas/automated1/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -nogaps > test_msas/nogaps/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -noallgaps > test_msas/noallgaps/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -gappyout > test_msas/gappyout/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -strict > test_msas/strict/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -strictplus > test_msas/strictplus/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -automated1 > test_msas/automated1/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -nogaps > test_msas/nogaps/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -noallgaps > test_msas/noallgaps/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -gappyout > test_msas/gappyout/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -strict > test_msas/strict/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -strictplus > test_msas/strictplus/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -automated1 > test_msas/automated1/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -nogaps > test_msas/nogaps/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -noallgaps > test_msas/noallgaps/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -gappyout > test_msas/gappyout/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -strict > test_msas/strict/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -strictplus > test_msas/strictplus/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -automated1 > test_msas/automated1/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -nogaps > test_msas/nogaps/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -noallgaps > test_msas/noallgaps/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -gappyout > test_msas/gappyout/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -strict > test_msas/strict/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -strictplus > test_msas/strictplus/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -automated1 > test_msas/automated1/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -nogaps > test_msas/nogaps/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -noallgaps > test_msas/noallgaps/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -gappyout > test_msas/gappyout/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -strict > test_msas/strict/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -strictplus > test_msas/strictplus/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -automated1 > test_msas/automated1/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -nogaps > test_msas/nogaps/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -noallgaps > test_msas/noallgaps/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -gappyout > test_msas/gappyout/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -strict > test_msas/strict/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -strictplus > test_msas/strictplus/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -automated1 > test_msas/automated1/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -nogaps > test_msas/nogaps/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -noallgaps > test_msas/noallgaps/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -gappyout > test_msas/gappyout/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -strict > test_msas/strict/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -strictplus > test_msas/strictplus/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -automated1 > test_msas/automated1/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -nogaps > test_msas/nogaps/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -noallgaps > test_msas/noallgaps/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -gappyout > test_msas/gappyout/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -strict > test_msas/strict/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -strictplus > test_msas/strictplus/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -automated1 > test_msas/automated1/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -nogaps > test_msas/nogaps/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -noallgaps > test_msas/noallgaps/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -gappyout > test_msas/gappyout/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -strict > test_msas/strict/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -strictplus > test_msas/strictplus/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -automated1 > test_msas/automated1/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -nogaps > test_msas/nogaps/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -noallgaps > test_msas/noallgaps/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -gappyout > test_msas/gappyout/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -strict > test_msas/strict/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -strictplus > test_msas/strictplus/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -automated1 > test_msas/automated1/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -nogaps > test_msas/nogaps/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -noallgaps > test_msas/noallgaps/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -gappyout > test_msas/gappyout/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -strict > test_msas/strict/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -strictplus > test_msas/strictplus/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -automated1 > test_msas/automated1/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -nogaps > test_msas/nogaps/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -noallgaps > test_msas/noallgaps/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -gappyout > test_msas/gappyout/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -strict > test_msas/strict/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -strictplus > test_msas/strictplus/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -automated1 > test_msas/automated1/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -nogaps > test_msas/nogaps/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -noallgaps > test_msas/noallgaps/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -gappyout > test_msas/gappyout/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -strict > test_msas/strict/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -strictplus > test_msas/strictplus/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -automated1 > test_msas/automated1/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -nogaps > test_msas/nogaps/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -noallgaps > test_msas/noallgaps/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -gappyout > test_msas/gappyout/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -strict > test_msas/strict/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -strictplus > test_msas/strictplus/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -automated1 > test_msas/automated1/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -nogaps > test_msas/nogaps/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -noallgaps > test_msas/noallgaps/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -gappyout > test_msas/gappyout/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -strict > test_msas/strict/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -strictplus > test_msas/strictplus/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -automated1 > test_msas/automated1/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -nogaps > test_msas/nogaps/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -noallgaps > test_msas/noallgaps/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -gappyout > test_msas/gappyout/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -strict > test_msas/strict/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -strictplus > test_msas/strictplus/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -automated1 > test_msas/automated1/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -nogaps > test_msas/nogaps/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -noallgaps > test_msas/noallgaps/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -gappyout > test_msas/gappyout/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -strict > test_msas/strict/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -strictplus > test_msas/strictplus/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -automated1 > test_msas/automated1/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -nogaps > test_msas/nogaps/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -noallgaps > test_msas/noallgaps/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -gappyout > test_msas/gappyout/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -strict > test_msas/strict/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -strictplus > test_msas/strictplus/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -automated1 > test_msas/automated1/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -nogaps > test_msas/nogaps/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -noallgaps > test_msas/noallgaps/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -gappyout > test_msas/gappyout/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -strict > test_msas/strict/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -strictplus > test_msas/strictplus/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -automated1 > test_msas/automated1/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -nogaps > test_msas/nogaps/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -noallgaps > test_msas/noallgaps/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -gappyout > test_msas/gappyout/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -strict > test_msas/strict/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -strictplus > test_msas/strictplus/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -automated1 > test_msas/automated1/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -nogaps > test_msas/nogaps/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -noallgaps > test_msas/noallgaps/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -gappyout > test_msas/gappyout/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -strict > test_msas/strict/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -strictplus > test_msas/strictplus/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -automated1 > test_msas/automated1/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -nogaps > test_msas/nogaps/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -noallgaps > test_msas/noallgaps/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -gappyout > test_msas/gappyout/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -strict > test_msas/strict/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -strictplus > test_msas/strictplus/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -automated1 > test_msas/automated1/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -nogaps > test_msas/nogaps/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -noallgaps > test_msas/noallgaps/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -gappyout > test_msas/gappyout/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -strict > test_msas/strict/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -strictplus > test_msas/strictplus/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -automated1 > test_msas/automated1/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -nogaps > test_msas/nogaps/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -noallgaps > test_msas/noallgaps/example.091.AA.strNOG.ENOG411BWBU.fasta From f493510352d92078f1beb1c7b0d36f9fed380a02 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Fri, 9 Aug 2024 15:00:45 +0200 Subject: [PATCH 35/61] Update test script to be run --- .github/workflows/build.yml | 31 ++----------------------------- 1 file changed, 2 insertions(+), 29 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 15aa8cba1..20dc0d6a0 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -13,37 +13,10 @@ on: name: Build jobs: - download_and_test_windows: - runs-on: windows-2022 - steps: - - uses: actions/checkout@v4 - - name: Download Release Binaries - run: | - curl -L -o trimal.zip https://github.com/inab/trimal/releases/download/v1.5.0/trimAl_Windows_x86-64.zip - - - name: Unzip Binaries - run: | - powershell -Command "Expand-Archive -Path trimal.zip -DestinationPath ." - - name: List Directory Contents - run: | - dir .\ - - - name: Verify Binaries - run: | - # Use PowerShell or native Windows commands to verify binaries - Get-Command .\trimal.exe - - - name: Run generate_trimmed_msas.ps1 - run: | - powershell -ExecutionPolicy Bypass -File .\scripts\generate_trimmed_msas.ps1 - - - name: Run compare_trimmed_msas.ps1 - run: | - powershell -ExecutionPolicy Bypass -File .\scripts\compare_trimmed_msas.ps1 build_and_test_windows: runs-on: windows-2022 steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up MSYS2 uses: msys2/setup-msys2@v2 with: @@ -61,7 +34,7 @@ jobs: file readal.exe file statal.exe cd .. - bash scripts/generate_trimmed_msas.sh + bash scripts/generate_trimmed_msas_Windows.sh echo "test_msas/gappyout/example.004.AA.fasta" cat test_msas/gappyout/example.004.AA.fasta echo "dataset/trimmed_msas/gappyout/example.004.AA.fasta" From 5d7712457fba451746892f0a880e3293cc3a35be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Fri, 9 Aug 2024 15:00:56 +0200 Subject: [PATCH 36/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 30096e3de..1f9a8f15a 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched +Temporary file to force Github Actions workflow to be launched. From 973d15422d78854127d5f68c16a1abffc9219429 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 09:34:02 +0200 Subject: [PATCH 37/61] Debug Windows compilation test --- .github/workflows/build.yml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 20dc0d6a0..075bcf1bb 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -34,9 +34,4 @@ jobs: file readal.exe file statal.exe cd .. - bash scripts/generate_trimmed_msas_Windows.sh - echo "test_msas/gappyout/example.004.AA.fasta" - cat test_msas/gappyout/example.004.AA.fasta - echo "dataset/trimmed_msas/gappyout/example.004.AA.fasta" - cat dataset/trimmed_msas/gappyout/example.004.AA.fasta - bash scripts/compare_trimmed_msas.sh + ./source/trimal.exe -in dataset/example.004.AA.fasta -gappyout From c4224b4c57f2bf03df8be94df5e997fde03967bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 09:34:22 +0200 Subject: [PATCH 38/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 1f9a8f15a..30096e3de 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched. +Temporary file to force Github Actions workflow to be launched From 28439a4fbb83c40af35a7530883dfab8bcd6e0a3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 09:44:35 +0200 Subject: [PATCH 39/61] Update build.yml --- .github/workflows/build.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 075bcf1bb..e4a5c19dd 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -34,4 +34,5 @@ jobs: file readal.exe file statal.exe cd .. - ./source/trimal.exe -in dataset/example.004.AA.fasta -gappyout + ./source/trimal.exe -in dataset/example.004.AA.fasta -gappyout > test_msas/gappyout/example.004.AA.fasta + cat test_msas/gappyout/example.004.AA.fasta From 46000c5bbf6eed3f2857fb4d55bc7c615c563cb7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 09:44:48 +0200 Subject: [PATCH 40/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 30096e3de..1f9a8f15a 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched +Temporary file to force Github Actions workflow to be launched. From 1347d913ffd7f8bad1017027fb4ec837de2773c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 10:02:31 +0200 Subject: [PATCH 41/61] Update build.yml --- .github/workflows/build.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index e4a5c19dd..2a776d82c 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -34,5 +34,7 @@ jobs: file readal.exe file statal.exe cd .. + mkdir test_msas + mkdir test_msas/gappyout ./source/trimal.exe -in dataset/example.004.AA.fasta -gappyout > test_msas/gappyout/example.004.AA.fasta cat test_msas/gappyout/example.004.AA.fasta From 9c70f185926c8ab2e7d29cfb9dbb04564266a4e6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 10:02:41 +0200 Subject: [PATCH 42/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 1f9a8f15a..30096e3de 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched. +Temporary file to force Github Actions workflow to be launched From fe8b5b6cba817f9c25ebe993c534bfa5befef0bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 10:15:12 +0200 Subject: [PATCH 43/61] Delete scripts/generate_trimmed_msas_Windows.sh --- scripts/generate_trimmed_msas_Windows.sh | 512 ----------------------- 1 file changed, 512 deletions(-) delete mode 100644 scripts/generate_trimmed_msas_Windows.sh diff --git a/scripts/generate_trimmed_msas_Windows.sh b/scripts/generate_trimmed_msas_Windows.sh deleted file mode 100644 index cba5b3ed2..000000000 --- a/scripts/generate_trimmed_msas_Windows.sh +++ /dev/null @@ -1,512 +0,0 @@ -mkdir test_msas -mkdir test_msas/gappyout -mkdir test_msas/strict -mkdir test_msas/strictplus -mkdir test_msas/automated1 -mkdir test_msas/nogaps -mkdir test_msas/noallgaps - -./source/trimal.exe -in dataset/example.004.AA.fasta -gappyout > test_msas/gappyout/example.004.AA.fasta -./source/trimal.exe -in dataset/example.004.AA.fasta -strict > test_msas/strict/example.004.AA.fasta -./source/trimal.exe -in dataset/example.004.AA.fasta -strictplus > test_msas/strictplus/example.004.AA.fasta -./source/trimal.exe -in dataset/example.004.AA.fasta -automated1 > test_msas/automated1/example.004.AA.fasta -./source/trimal.exe -in dataset/example.004.AA.fasta -nogaps > test_msas/nogaps/example.004.AA.fasta -./source/trimal.exe -in dataset/example.004.AA.fasta -noallgaps > test_msas/noallgaps/example.004.AA.fasta -./source/trimal.exe -in dataset/example.005.AA.fasta -gappyout > test_msas/gappyout/example.005.AA.fasta -./source/trimal.exe -in dataset/example.005.AA.fasta -strict > test_msas/strict/example.005.AA.fasta -./source/trimal.exe -in dataset/example.005.AA.fasta -strictplus > test_msas/strictplus/example.005.AA.fasta -./source/trimal.exe -in dataset/example.005.AA.fasta -automated1 > test_msas/automated1/example.005.AA.fasta -./source/trimal.exe -in dataset/example.005.AA.fasta -nogaps > test_msas/nogaps/example.005.AA.fasta -./source/trimal.exe -in dataset/example.005.AA.fasta -noallgaps > test_msas/noallgaps/example.005.AA.fasta -./source/trimal.exe -in dataset/example.007.AA.fasta -gappyout > test_msas/gappyout/example.007.AA.fasta -./source/trimal.exe -in dataset/example.007.AA.fasta -strict > test_msas/strict/example.007.AA.fasta -./source/trimal.exe -in dataset/example.007.AA.fasta -strictplus > test_msas/strictplus/example.007.AA.fasta -./source/trimal.exe -in dataset/example.007.AA.fasta -automated1 > test_msas/automated1/example.007.AA.fasta -./source/trimal.exe -in dataset/example.007.AA.fasta -nogaps > test_msas/nogaps/example.007.AA.fasta -./source/trimal.exe -in dataset/example.007.AA.fasta -noallgaps > test_msas/noallgaps/example.007.AA.fasta -./source/trimal.exe -in dataset/example.009.AA.fasta -gappyout > test_msas/gappyout/example.009.AA.fasta -./source/trimal.exe -in dataset/example.009.AA.fasta -strict > test_msas/strict/example.009.AA.fasta -./source/trimal.exe -in dataset/example.009.AA.fasta -strictplus > test_msas/strictplus/example.009.AA.fasta -./source/trimal.exe -in dataset/example.009.AA.fasta -automated1 > test_msas/automated1/example.009.AA.fasta -./source/trimal.exe -in dataset/example.009.AA.fasta -nogaps > test_msas/nogaps/example.009.AA.fasta -./source/trimal.exe -in dataset/example.009.AA.fasta -noallgaps > test_msas/noallgaps/example.009.AA.fasta -./source/trimal.exe -in dataset/example.010.AA.fasta -gappyout > test_msas/gappyout/example.010.AA.fasta -./source/trimal.exe -in dataset/example.010.AA.fasta -strict > test_msas/strict/example.010.AA.fasta -./source/trimal.exe -in dataset/example.010.AA.fasta -strictplus > test_msas/strictplus/example.010.AA.fasta -./source/trimal.exe -in dataset/example.010.AA.fasta -automated1 > test_msas/automated1/example.010.AA.fasta -./source/trimal.exe -in dataset/example.010.AA.fasta -nogaps > test_msas/nogaps/example.010.AA.fasta -./source/trimal.exe -in dataset/example.010.AA.fasta -noallgaps > test_msas/noallgaps/example.010.AA.fasta -./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -gappyout > test_msas/gappyout/example.011.AA.YKL197C.fasta -./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -strict > test_msas/strict/example.011.AA.YKL197C.fasta -./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -strictplus > test_msas/strictplus/example.011.AA.YKL197C.fasta -./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -automated1 > test_msas/automated1/example.011.AA.YKL197C.fasta -./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -nogaps > test_msas/nogaps/example.011.AA.YKL197C.fasta -./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -noallgaps > test_msas/noallgaps/example.011.AA.YKL197C.fasta -./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -gappyout > test_msas/gappyout/example.014.AA.EggNOG.COG0591.fasta -./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -strict > test_msas/strict/example.014.AA.EggNOG.COG0591.fasta -./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -strictplus > test_msas/strictplus/example.014.AA.EggNOG.COG0591.fasta -./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -automated1 > test_msas/automated1/example.014.AA.EggNOG.COG0591.fasta -./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -nogaps > test_msas/nogaps/example.014.AA.EggNOG.COG0591.fasta -./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -noallgaps > test_msas/noallgaps/example.014.AA.EggNOG.COG0591.fasta -./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -gappyout > test_msas/gappyout/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -strict > test_msas/strict/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -strictplus > test_msas/strictplus/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -automated1 > test_msas/automated1/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -nogaps > test_msas/nogaps/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -noallgaps > test_msas/noallgaps/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -gappyout > test_msas/gappyout/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -strict > test_msas/strict/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -strictplus > test_msas/strictplus/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -automated1 > test_msas/automated1/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -nogaps > test_msas/nogaps/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -noallgaps > test_msas/noallgaps/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -gappyout > test_msas/gappyout/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -strict > test_msas/strict/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -strictplus > test_msas/strictplus/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -automated1 > test_msas/automated1/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -nogaps > test_msas/nogaps/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -noallgaps > test_msas/noallgaps/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -gappyout > test_msas/gappyout/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -strict > test_msas/strict/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -strictplus > test_msas/strictplus/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -automated1 > test_msas/automated1/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -nogaps > test_msas/nogaps/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -noallgaps > test_msas/noallgaps/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -gappyout > test_msas/gappyout/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -strict > test_msas/strict/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -strictplus > test_msas/strictplus/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -automated1 > test_msas/automated1/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -nogaps > test_msas/nogaps/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -noallgaps > test_msas/noallgaps/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -gappyout > test_msas/gappyout/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -strict > test_msas/strict/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -strictplus > test_msas/strictplus/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -automated1 > test_msas/automated1/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -nogaps > test_msas/nogaps/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -noallgaps > test_msas/noallgaps/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -gappyout > test_msas/gappyout/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -strict > test_msas/strict/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -strictplus > test_msas/strictplus/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -automated1 > test_msas/automated1/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -nogaps > test_msas/nogaps/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -noallgaps > test_msas/noallgaps/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -gappyout > test_msas/gappyout/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -strict > test_msas/strict/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -strictplus > test_msas/strictplus/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -automated1 > test_msas/automated1/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -nogaps > test_msas/nogaps/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -noallgaps > test_msas/noallgaps/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -gappyout > test_msas/gappyout/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -strict > test_msas/strict/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -strictplus > test_msas/strictplus/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -automated1 > test_msas/automated1/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -nogaps > test_msas/nogaps/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -noallgaps > test_msas/noallgaps/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -gappyout > test_msas/gappyout/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -strict > test_msas/strict/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -strictplus > test_msas/strictplus/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -automated1 > test_msas/automated1/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -nogaps > test_msas/nogaps/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -noallgaps > test_msas/noallgaps/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -gappyout > test_msas/gappyout/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -strict > test_msas/strict/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -strictplus > test_msas/strictplus/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -automated1 > test_msas/automated1/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -nogaps > test_msas/nogaps/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -noallgaps > test_msas/noallgaps/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -gappyout > test_msas/gappyout/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -strict > test_msas/strict/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -strictplus > test_msas/strictplus/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -automated1 > test_msas/automated1/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -nogaps > test_msas/nogaps/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -noallgaps > test_msas/noallgaps/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -gappyout > test_msas/gappyout/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -strict > test_msas/strict/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -strictplus > test_msas/strictplus/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -automated1 > test_msas/automated1/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -nogaps > test_msas/nogaps/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -noallgaps > test_msas/noallgaps/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -gappyout > test_msas/gappyout/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -strict > test_msas/strict/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -strictplus > test_msas/strictplus/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -automated1 > test_msas/automated1/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -nogaps > test_msas/nogaps/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -noallgaps > test_msas/noallgaps/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -gappyout > test_msas/gappyout/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -strict > test_msas/strict/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -strictplus > test_msas/strictplus/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -automated1 > test_msas/automated1/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -nogaps > test_msas/nogaps/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -noallgaps > test_msas/noallgaps/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -gappyout > test_msas/gappyout/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -strict > test_msas/strict/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -strictplus > test_msas/strictplus/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -automated1 > test_msas/automated1/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -nogaps > test_msas/nogaps/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -noallgaps > test_msas/noallgaps/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -gappyout > test_msas/gappyout/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -strict > test_msas/strict/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -strictplus > test_msas/strictplus/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -automated1 > test_msas/automated1/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -nogaps > test_msas/nogaps/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -noallgaps > test_msas/noallgaps/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -gappyout > test_msas/gappyout/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -strict > test_msas/strict/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -strictplus > test_msas/strictplus/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -automated1 > test_msas/automated1/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -nogaps > test_msas/nogaps/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -noallgaps > test_msas/noallgaps/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -gappyout > test_msas/gappyout/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -strict > test_msas/strict/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -strictplus > test_msas/strictplus/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -automated1 > test_msas/automated1/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -nogaps > test_msas/nogaps/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -noallgaps > test_msas/noallgaps/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -gappyout > test_msas/gappyout/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -strict > test_msas/strict/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -strictplus > test_msas/strictplus/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -automated1 > test_msas/automated1/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -nogaps > test_msas/nogaps/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -noallgaps > test_msas/noallgaps/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -gappyout > test_msas/gappyout/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -strict > test_msas/strict/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -strictplus > test_msas/strictplus/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -automated1 > test_msas/automated1/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -nogaps > test_msas/nogaps/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -noallgaps > test_msas/noallgaps/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -gappyout > test_msas/gappyout/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -strict > test_msas/strict/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -strictplus > test_msas/strictplus/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -automated1 > test_msas/automated1/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -nogaps > test_msas/nogaps/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -noallgaps > test_msas/noallgaps/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -gappyout > test_msas/gappyout/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -strict > test_msas/strict/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -strictplus > test_msas/strictplus/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -automated1 > test_msas/automated1/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -nogaps > test_msas/nogaps/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -noallgaps > test_msas/noallgaps/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -gappyout > test_msas/gappyout/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -strict > test_msas/strict/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -strictplus > test_msas/strictplus/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -automated1 > test_msas/automated1/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -nogaps > test_msas/nogaps/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -noallgaps > test_msas/noallgaps/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -gappyout > test_msas/gappyout/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -strict > test_msas/strict/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -strictplus > test_msas/strictplus/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -automated1 > test_msas/automated1/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -nogaps > test_msas/nogaps/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -noallgaps > test_msas/noallgaps/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -gappyout > test_msas/gappyout/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -strict > test_msas/strict/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -strictplus > test_msas/strictplus/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -automated1 > test_msas/automated1/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -nogaps > test_msas/nogaps/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -noallgaps > test_msas/noallgaps/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -gappyout > test_msas/gappyout/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -strict > test_msas/strict/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -strictplus > test_msas/strictplus/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -automated1 > test_msas/automated1/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -nogaps > test_msas/nogaps/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -noallgaps > test_msas/noallgaps/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -gappyout > test_msas/gappyout/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -strict > test_msas/strict/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -strictplus > test_msas/strictplus/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -automated1 > test_msas/automated1/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -nogaps > test_msas/nogaps/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -noallgaps > test_msas/noallgaps/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -gappyout > test_msas/gappyout/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -strict > test_msas/strict/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -strictplus > test_msas/strictplus/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -automated1 > test_msas/automated1/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -nogaps > test_msas/nogaps/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -noallgaps > test_msas/noallgaps/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -gappyout > test_msas/gappyout/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -strict > test_msas/strict/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -strictplus > test_msas/strictplus/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -automated1 > test_msas/automated1/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -nogaps > test_msas/nogaps/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -noallgaps > test_msas/noallgaps/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -gappyout > test_msas/gappyout/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -strict > test_msas/strict/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -strictplus > test_msas/strictplus/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -automated1 > test_msas/automated1/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -nogaps > test_msas/nogaps/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -noallgaps > test_msas/noallgaps/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -gappyout > test_msas/gappyout/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -strict > test_msas/strict/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -strictplus > test_msas/strictplus/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -automated1 > test_msas/automated1/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -nogaps > test_msas/nogaps/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -noallgaps > test_msas/noallgaps/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -gappyout > test_msas/gappyout/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -strict > test_msas/strict/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -strictplus > test_msas/strictplus/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -automated1 > test_msas/automated1/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -nogaps > test_msas/nogaps/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -noallgaps > test_msas/noallgaps/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -gappyout > test_msas/gappyout/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strict > test_msas/strict/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strictplus > test_msas/strictplus/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -automated1 > test_msas/automated1/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -nogaps > test_msas/nogaps/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -noallgaps > test_msas/noallgaps/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -gappyout > test_msas/gappyout/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -strict > test_msas/strict/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -strictplus > test_msas/strictplus/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -automated1 > test_msas/automated1/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -nogaps > test_msas/nogaps/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -noallgaps > test_msas/noallgaps/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -gappyout > test_msas/gappyout/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strict > test_msas/strict/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strictplus > test_msas/strictplus/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -automated1 > test_msas/automated1/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -nogaps > test_msas/nogaps/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -noallgaps > test_msas/noallgaps/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -gappyout > test_msas/gappyout/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strict > test_msas/strict/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strictplus > test_msas/strictplus/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -automated1 > test_msas/automated1/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -nogaps > test_msas/nogaps/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -noallgaps > test_msas/noallgaps/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -gappyout > test_msas/gappyout/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -strict > test_msas/strict/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -strictplus > test_msas/strictplus/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -automated1 > test_msas/automated1/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -nogaps > test_msas/nogaps/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -noallgaps > test_msas/noallgaps/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -gappyout > test_msas/gappyout/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -strict > test_msas/strict/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -strictplus > test_msas/strictplus/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -automated1 > test_msas/automated1/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -nogaps > test_msas/nogaps/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -noallgaps > test_msas/noallgaps/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -gappyout > test_msas/gappyout/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -strict > test_msas/strict/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -strictplus > test_msas/strictplus/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -automated1 > test_msas/automated1/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -nogaps > test_msas/nogaps/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -noallgaps > test_msas/noallgaps/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -gappyout > test_msas/gappyout/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -strict > test_msas/strict/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -strictplus > test_msas/strictplus/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -automated1 > test_msas/automated1/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -nogaps > test_msas/nogaps/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -noallgaps > test_msas/noallgaps/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -gappyout > test_msas/gappyout/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strict > test_msas/strict/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strictplus > test_msas/strictplus/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -automated1 > test_msas/automated1/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -nogaps > test_msas/nogaps/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -noallgaps > test_msas/noallgaps/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -gappyout > test_msas/gappyout/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strict > test_msas/strict/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strictplus > test_msas/strictplus/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -automated1 > test_msas/automated1/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -nogaps > test_msas/nogaps/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -noallgaps > test_msas/noallgaps/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -gappyout > test_msas/gappyout/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -strict > test_msas/strict/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -strictplus > test_msas/strictplus/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -automated1 > test_msas/automated1/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -nogaps > test_msas/nogaps/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -noallgaps > test_msas/noallgaps/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -gappyout > test_msas/gappyout/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -strict > test_msas/strict/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -strictplus > test_msas/strictplus/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -automated1 > test_msas/automated1/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -nogaps > test_msas/nogaps/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -noallgaps > test_msas/noallgaps/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -gappyout > test_msas/gappyout/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -strict > test_msas/strict/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -strictplus > test_msas/strictplus/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -automated1 > test_msas/automated1/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -nogaps > test_msas/nogaps/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -noallgaps > test_msas/noallgaps/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -gappyout > test_msas/gappyout/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -strict > test_msas/strict/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -strictplus > test_msas/strictplus/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -automated1 > test_msas/automated1/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -nogaps > test_msas/nogaps/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -noallgaps > test_msas/noallgaps/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -gappyout > test_msas/gappyout/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -strict > test_msas/strict/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -strictplus > test_msas/strictplus/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -automated1 > test_msas/automated1/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -nogaps > test_msas/nogaps/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -noallgaps > test_msas/noallgaps/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -gappyout > test_msas/gappyout/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -strict > test_msas/strict/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -strictplus > test_msas/strictplus/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -automated1 > test_msas/automated1/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -nogaps > test_msas/nogaps/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -noallgaps > test_msas/noallgaps/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -gappyout > test_msas/gappyout/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -strict > test_msas/strict/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -strictplus > test_msas/strictplus/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -automated1 > test_msas/automated1/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -nogaps > test_msas/nogaps/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -noallgaps > test_msas/noallgaps/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -gappyout > test_msas/gappyout/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -strict > test_msas/strict/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -strictplus > test_msas/strictplus/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -automated1 > test_msas/automated1/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -nogaps > test_msas/nogaps/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -noallgaps > test_msas/noallgaps/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -gappyout > test_msas/gappyout/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -strict > test_msas/strict/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -strictplus > test_msas/strictplus/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -automated1 > test_msas/automated1/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -nogaps > test_msas/nogaps/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -noallgaps > test_msas/noallgaps/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -gappyout > test_msas/gappyout/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -strict > test_msas/strict/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -strictplus > test_msas/strictplus/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -automated1 > test_msas/automated1/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -nogaps > test_msas/nogaps/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -noallgaps > test_msas/noallgaps/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -gappyout > test_msas/gappyout/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -strict > test_msas/strict/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -strictplus > test_msas/strictplus/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -automated1 > test_msas/automated1/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -nogaps > test_msas/nogaps/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -noallgaps > test_msas/noallgaps/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -gappyout > test_msas/gappyout/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -strict > test_msas/strict/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -strictplus > test_msas/strictplus/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -automated1 > test_msas/automated1/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -nogaps > test_msas/nogaps/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -noallgaps > test_msas/noallgaps/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -gappyout > test_msas/gappyout/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -strict > test_msas/strict/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -strictplus > test_msas/strictplus/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -automated1 > test_msas/automated1/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -nogaps > test_msas/nogaps/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -noallgaps > test_msas/noallgaps/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -gappyout > test_msas/gappyout/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -strict > test_msas/strict/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -strictplus > test_msas/strictplus/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -automated1 > test_msas/automated1/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -nogaps > test_msas/nogaps/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -noallgaps > test_msas/noallgaps/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -gappyout > test_msas/gappyout/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -strict > test_msas/strict/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -strictplus > test_msas/strictplus/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -automated1 > test_msas/automated1/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -nogaps > test_msas/nogaps/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -noallgaps > test_msas/noallgaps/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -gappyout > test_msas/gappyout/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -strict > test_msas/strict/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -strictplus > test_msas/strictplus/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -automated1 > test_msas/automated1/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -nogaps > test_msas/nogaps/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -noallgaps > test_msas/noallgaps/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -gappyout > test_msas/gappyout/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -strict > test_msas/strict/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -strictplus > test_msas/strictplus/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -automated1 > test_msas/automated1/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -nogaps > test_msas/nogaps/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -noallgaps > test_msas/noallgaps/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -gappyout > test_msas/gappyout/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -strict > test_msas/strict/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -strictplus > test_msas/strictplus/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -automated1 > test_msas/automated1/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -nogaps > test_msas/nogaps/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -noallgaps > test_msas/noallgaps/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -gappyout > test_msas/gappyout/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -strict > test_msas/strict/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -strictplus > test_msas/strictplus/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -automated1 > test_msas/automated1/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -nogaps > test_msas/nogaps/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -noallgaps > test_msas/noallgaps/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -gappyout > test_msas/gappyout/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -strict > test_msas/strict/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -strictplus > test_msas/strictplus/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -automated1 > test_msas/automated1/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -nogaps > test_msas/nogaps/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -noallgaps > test_msas/noallgaps/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -gappyout > test_msas/gappyout/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -strict > test_msas/strict/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -strictplus > test_msas/strictplus/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -automated1 > test_msas/automated1/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -nogaps > test_msas/nogaps/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -noallgaps > test_msas/noallgaps/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -gappyout > test_msas/gappyout/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -strict > test_msas/strict/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -strictplus > test_msas/strictplus/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -automated1 > test_msas/automated1/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -nogaps > test_msas/nogaps/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -noallgaps > test_msas/noallgaps/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -gappyout > test_msas/gappyout/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -strict > test_msas/strict/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -strictplus > test_msas/strictplus/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -automated1 > test_msas/automated1/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -nogaps > test_msas/nogaps/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -noallgaps > test_msas/noallgaps/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -gappyout > test_msas/gappyout/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -strict > test_msas/strict/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -strictplus > test_msas/strictplus/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -automated1 > test_msas/automated1/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -nogaps > test_msas/nogaps/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -noallgaps > test_msas/noallgaps/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -gappyout > test_msas/gappyout/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -strict > test_msas/strict/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -strictplus > test_msas/strictplus/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -automated1 > test_msas/automated1/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -nogaps > test_msas/nogaps/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -noallgaps > test_msas/noallgaps/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -gappyout > test_msas/gappyout/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -strict > test_msas/strict/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -strictplus > test_msas/strictplus/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -automated1 > test_msas/automated1/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -nogaps > test_msas/nogaps/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -noallgaps > test_msas/noallgaps/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -gappyout > test_msas/gappyout/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -strict > test_msas/strict/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -strictplus > test_msas/strictplus/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -automated1 > test_msas/automated1/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -nogaps > test_msas/nogaps/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -noallgaps > test_msas/noallgaps/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -gappyout > test_msas/gappyout/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -strict > test_msas/strict/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -strictplus > test_msas/strictplus/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -automated1 > test_msas/automated1/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -nogaps > test_msas/nogaps/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -noallgaps > test_msas/noallgaps/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -gappyout > test_msas/gappyout/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -strict > test_msas/strict/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -strictplus > test_msas/strictplus/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -automated1 > test_msas/automated1/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -nogaps > test_msas/nogaps/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -noallgaps > test_msas/noallgaps/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -gappyout > test_msas/gappyout/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -strict > test_msas/strict/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -strictplus > test_msas/strictplus/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -automated1 > test_msas/automated1/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -nogaps > test_msas/nogaps/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -noallgaps > test_msas/noallgaps/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -gappyout > test_msas/gappyout/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -strict > test_msas/strict/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -strictplus > test_msas/strictplus/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -automated1 > test_msas/automated1/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -nogaps > test_msas/nogaps/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -noallgaps > test_msas/noallgaps/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -gappyout > test_msas/gappyout/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -strict > test_msas/strict/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -strictplus > test_msas/strictplus/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -automated1 > test_msas/automated1/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -nogaps > test_msas/nogaps/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -noallgaps > test_msas/noallgaps/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -gappyout > test_msas/gappyout/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -strict > test_msas/strict/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -strictplus > test_msas/strictplus/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -automated1 > test_msas/automated1/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -nogaps > test_msas/nogaps/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -noallgaps > test_msas/noallgaps/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -gappyout > test_msas/gappyout/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -strict > test_msas/strict/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -strictplus > test_msas/strictplus/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -automated1 > test_msas/automated1/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -nogaps > test_msas/nogaps/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -noallgaps > test_msas/noallgaps/example.091.AA.strNOG.ENOG411BWBU.fasta From 00d0a4b690032b693ed90dd904df16e36d860333 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 10:17:36 +0200 Subject: [PATCH 44/61] Update build.yml --- .github/workflows/build.yml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 2a776d82c..5e983aed5 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -33,8 +33,10 @@ jobs: file trimal.exe file readal.exe file statal.exe - cd .. - mkdir test_msas - mkdir test_msas/gappyout - ./source/trimal.exe -in dataset/example.004.AA.fasta -gappyout > test_msas/gappyout/example.004.AA.fasta - cat test_msas/gappyout/example.004.AA.fasta + - name: Run generate_trimmed_msas.ps1 + run: | + powershell -ExecutionPolicy Bypass -File .\scripts\generate_trimmed_msas.ps1 + + - name: Run compare_trimmed_msas.ps1 + run: | + powershell -ExecutionPolicy Bypass -File .\scripts\compare_trimmed_msas.ps1 From 2839828bcc977b26a1025b6847a6c4a56753dd3d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 10:17:46 +0200 Subject: [PATCH 45/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 30096e3de..1f9a8f15a 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched +Temporary file to force Github Actions workflow to be launched. From c30236f6bfe6d3c1591ad14e611ba73a62720943 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 10:22:30 +0200 Subject: [PATCH 46/61] Add generate_trimmed_msas_Windows.sh --- scripts/generate_trimmed_msas_Windows.sh | 512 +++++++++++++++++++++++ 1 file changed, 512 insertions(+) create mode 100644 scripts/generate_trimmed_msas_Windows.sh diff --git a/scripts/generate_trimmed_msas_Windows.sh b/scripts/generate_trimmed_msas_Windows.sh new file mode 100644 index 000000000..cba5b3ed2 --- /dev/null +++ b/scripts/generate_trimmed_msas_Windows.sh @@ -0,0 +1,512 @@ +mkdir test_msas +mkdir test_msas/gappyout +mkdir test_msas/strict +mkdir test_msas/strictplus +mkdir test_msas/automated1 +mkdir test_msas/nogaps +mkdir test_msas/noallgaps + +./source/trimal.exe -in dataset/example.004.AA.fasta -gappyout > test_msas/gappyout/example.004.AA.fasta +./source/trimal.exe -in dataset/example.004.AA.fasta -strict > test_msas/strict/example.004.AA.fasta +./source/trimal.exe -in dataset/example.004.AA.fasta -strictplus > test_msas/strictplus/example.004.AA.fasta +./source/trimal.exe -in dataset/example.004.AA.fasta -automated1 > test_msas/automated1/example.004.AA.fasta +./source/trimal.exe -in dataset/example.004.AA.fasta -nogaps > test_msas/nogaps/example.004.AA.fasta +./source/trimal.exe -in dataset/example.004.AA.fasta -noallgaps > test_msas/noallgaps/example.004.AA.fasta +./source/trimal.exe -in dataset/example.005.AA.fasta -gappyout > test_msas/gappyout/example.005.AA.fasta +./source/trimal.exe -in dataset/example.005.AA.fasta -strict > test_msas/strict/example.005.AA.fasta +./source/trimal.exe -in dataset/example.005.AA.fasta -strictplus > test_msas/strictplus/example.005.AA.fasta +./source/trimal.exe -in dataset/example.005.AA.fasta -automated1 > test_msas/automated1/example.005.AA.fasta +./source/trimal.exe -in dataset/example.005.AA.fasta -nogaps > test_msas/nogaps/example.005.AA.fasta +./source/trimal.exe -in dataset/example.005.AA.fasta -noallgaps > test_msas/noallgaps/example.005.AA.fasta +./source/trimal.exe -in dataset/example.007.AA.fasta -gappyout > test_msas/gappyout/example.007.AA.fasta +./source/trimal.exe -in dataset/example.007.AA.fasta -strict > test_msas/strict/example.007.AA.fasta +./source/trimal.exe -in dataset/example.007.AA.fasta -strictplus > test_msas/strictplus/example.007.AA.fasta +./source/trimal.exe -in dataset/example.007.AA.fasta -automated1 > test_msas/automated1/example.007.AA.fasta +./source/trimal.exe -in dataset/example.007.AA.fasta -nogaps > test_msas/nogaps/example.007.AA.fasta +./source/trimal.exe -in dataset/example.007.AA.fasta -noallgaps > test_msas/noallgaps/example.007.AA.fasta +./source/trimal.exe -in dataset/example.009.AA.fasta -gappyout > test_msas/gappyout/example.009.AA.fasta +./source/trimal.exe -in dataset/example.009.AA.fasta -strict > test_msas/strict/example.009.AA.fasta +./source/trimal.exe -in dataset/example.009.AA.fasta -strictplus > test_msas/strictplus/example.009.AA.fasta +./source/trimal.exe -in dataset/example.009.AA.fasta -automated1 > test_msas/automated1/example.009.AA.fasta +./source/trimal.exe -in dataset/example.009.AA.fasta -nogaps > test_msas/nogaps/example.009.AA.fasta +./source/trimal.exe -in dataset/example.009.AA.fasta -noallgaps > test_msas/noallgaps/example.009.AA.fasta +./source/trimal.exe -in dataset/example.010.AA.fasta -gappyout > test_msas/gappyout/example.010.AA.fasta +./source/trimal.exe -in dataset/example.010.AA.fasta -strict > test_msas/strict/example.010.AA.fasta +./source/trimal.exe -in dataset/example.010.AA.fasta -strictplus > test_msas/strictplus/example.010.AA.fasta +./source/trimal.exe -in dataset/example.010.AA.fasta -automated1 > test_msas/automated1/example.010.AA.fasta +./source/trimal.exe -in dataset/example.010.AA.fasta -nogaps > test_msas/nogaps/example.010.AA.fasta +./source/trimal.exe -in dataset/example.010.AA.fasta -noallgaps > test_msas/noallgaps/example.010.AA.fasta +./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -gappyout > test_msas/gappyout/example.011.AA.YKL197C.fasta +./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -strict > test_msas/strict/example.011.AA.YKL197C.fasta +./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -strictplus > test_msas/strictplus/example.011.AA.YKL197C.fasta +./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -automated1 > test_msas/automated1/example.011.AA.YKL197C.fasta +./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -nogaps > test_msas/nogaps/example.011.AA.YKL197C.fasta +./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -noallgaps > test_msas/noallgaps/example.011.AA.YKL197C.fasta +./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -gappyout > test_msas/gappyout/example.014.AA.EggNOG.COG0591.fasta +./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -strict > test_msas/strict/example.014.AA.EggNOG.COG0591.fasta +./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -strictplus > test_msas/strictplus/example.014.AA.EggNOG.COG0591.fasta +./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -automated1 > test_msas/automated1/example.014.AA.EggNOG.COG0591.fasta +./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -nogaps > test_msas/nogaps/example.014.AA.EggNOG.COG0591.fasta +./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -noallgaps > test_msas/noallgaps/example.014.AA.EggNOG.COG0591.fasta +./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -gappyout > test_msas/gappyout/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -strict > test_msas/strict/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -strictplus > test_msas/strictplus/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -automated1 > test_msas/automated1/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -nogaps > test_msas/nogaps/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -noallgaps > test_msas/noallgaps/example.015.AA.bctoNOG.ENOG41099F3.fasta +./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -gappyout > test_msas/gappyout/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -strict > test_msas/strict/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -strictplus > test_msas/strictplus/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -automated1 > test_msas/automated1/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -nogaps > test_msas/nogaps/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -noallgaps > test_msas/noallgaps/example.016.AA.bctoNOG.ENOG41099FB.fasta +./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -gappyout > test_msas/gappyout/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -strict > test_msas/strict/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -strictplus > test_msas/strictplus/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -automated1 > test_msas/automated1/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -nogaps > test_msas/nogaps/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -noallgaps > test_msas/noallgaps/example.017.AA.bctoNOG.ENOG41099FJ.fasta +./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -gappyout > test_msas/gappyout/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -strict > test_msas/strict/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -strictplus > test_msas/strictplus/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -automated1 > test_msas/automated1/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -nogaps > test_msas/nogaps/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -noallgaps > test_msas/noallgaps/example.018.AA.bctoNOG.ENOG41099FV.fasta +./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -gappyout > test_msas/gappyout/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -strict > test_msas/strict/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -strictplus > test_msas/strictplus/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -automated1 > test_msas/automated1/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -nogaps > test_msas/nogaps/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -noallgaps > test_msas/noallgaps/example.019.AA.bctoNOG.ENOG41099HI.fasta +./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -gappyout > test_msas/gappyout/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -strict > test_msas/strict/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -strictplus > test_msas/strictplus/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -automated1 > test_msas/automated1/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -nogaps > test_msas/nogaps/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -noallgaps > test_msas/noallgaps/example.020.AA.bctoNOG.ENOG41099HN.fasta +./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -gappyout > test_msas/gappyout/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -strict > test_msas/strict/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -strictplus > test_msas/strictplus/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -automated1 > test_msas/automated1/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -nogaps > test_msas/nogaps/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -noallgaps > test_msas/noallgaps/example.021.AA.bctoNOG.ENOG41099I5.fasta +./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -gappyout > test_msas/gappyout/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -strict > test_msas/strict/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -strictplus > test_msas/strictplus/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -automated1 > test_msas/automated1/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -nogaps > test_msas/nogaps/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -noallgaps > test_msas/noallgaps/example.022.AA.bctoNOG.ENOG41099IZ.fasta +./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -gappyout > test_msas/gappyout/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -strict > test_msas/strict/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -strictplus > test_msas/strictplus/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -automated1 > test_msas/automated1/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -nogaps > test_msas/nogaps/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -noallgaps > test_msas/noallgaps/example.023.AA.bctoNOG.ENOG41099K3.fasta +./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -gappyout > test_msas/gappyout/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -strict > test_msas/strict/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -strictplus > test_msas/strictplus/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -automated1 > test_msas/automated1/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -nogaps > test_msas/nogaps/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -noallgaps > test_msas/noallgaps/example.024.AA.bctoNOG.ENOG41099KM.fasta +./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -gappyout > test_msas/gappyout/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -strict > test_msas/strict/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -strictplus > test_msas/strictplus/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -automated1 > test_msas/automated1/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -nogaps > test_msas/nogaps/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -noallgaps > test_msas/noallgaps/example.025.AA.bctoNOG.ENOG41099KP.fasta +./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -gappyout > test_msas/gappyout/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -strict > test_msas/strict/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -strictplus > test_msas/strictplus/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -automated1 > test_msas/automated1/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -nogaps > test_msas/nogaps/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -noallgaps > test_msas/noallgaps/example.026.AA.bctoNOG.ENOG41099MV.fasta +./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -gappyout > test_msas/gappyout/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -strict > test_msas/strict/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -strictplus > test_msas/strictplus/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -automated1 > test_msas/automated1/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -nogaps > test_msas/nogaps/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -noallgaps > test_msas/noallgaps/example.027.AA.bctoNOG.ENOG41099NY.fasta +./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -gappyout > test_msas/gappyout/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -strict > test_msas/strict/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -strictplus > test_msas/strictplus/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -automated1 > test_msas/automated1/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -nogaps > test_msas/nogaps/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -noallgaps > test_msas/noallgaps/example.028.AA.bctoNOG.ENOG41099PA.fasta +./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -gappyout > test_msas/gappyout/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -strict > test_msas/strict/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -strictplus > test_msas/strictplus/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -automated1 > test_msas/automated1/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -nogaps > test_msas/nogaps/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -noallgaps > test_msas/noallgaps/example.029.AA.bctoNOG.ENOG41099Q3.fasta +./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -gappyout > test_msas/gappyout/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -strict > test_msas/strict/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -strictplus > test_msas/strictplus/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -automated1 > test_msas/automated1/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -nogaps > test_msas/nogaps/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -noallgaps > test_msas/noallgaps/example.030.AA.bctoNOG.ENOG41099RG.fasta +./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -gappyout > test_msas/gappyout/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -strict > test_msas/strict/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -strictplus > test_msas/strictplus/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -automated1 > test_msas/automated1/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -nogaps > test_msas/nogaps/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -noallgaps > test_msas/noallgaps/example.031.AA.bctoNOG.ENOG41099UK.fasta +./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -gappyout > test_msas/gappyout/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -strict > test_msas/strict/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -strictplus > test_msas/strictplus/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -automated1 > test_msas/automated1/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -nogaps > test_msas/nogaps/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -noallgaps > test_msas/noallgaps/example.032.AA.bctoNOG.ENOG41099UW.fasta +./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -gappyout > test_msas/gappyout/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -strict > test_msas/strict/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -strictplus > test_msas/strictplus/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -automated1 > test_msas/automated1/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -nogaps > test_msas/nogaps/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -noallgaps > test_msas/noallgaps/example.033.AA.bctoNOG.ENOG41099VK.fasta +./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -gappyout > test_msas/gappyout/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -strict > test_msas/strict/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -strictplus > test_msas/strictplus/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -automated1 > test_msas/automated1/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -nogaps > test_msas/nogaps/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -noallgaps > test_msas/noallgaps/example.034.AA.bctoNOG.ENOG41099WA.fasta +./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -gappyout > test_msas/gappyout/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -strict > test_msas/strict/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -strictplus > test_msas/strictplus/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -automated1 > test_msas/automated1/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -nogaps > test_msas/nogaps/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -noallgaps > test_msas/noallgaps/example.035.AA.bctoNOG.ENOG41099WF.fasta +./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -gappyout > test_msas/gappyout/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -strict > test_msas/strict/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -strictplus > test_msas/strictplus/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -automated1 > test_msas/automated1/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -nogaps > test_msas/nogaps/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -noallgaps > test_msas/noallgaps/example.036.AA.bctoNOG.ENOG41099XJ.fasta +./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -gappyout > test_msas/gappyout/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -strict > test_msas/strict/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -strictplus > test_msas/strictplus/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -automated1 > test_msas/automated1/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -nogaps > test_msas/nogaps/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -noallgaps > test_msas/noallgaps/example.037.AA.bctoNOG.ENOG41099XP.fasta +./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -gappyout > test_msas/gappyout/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -strict > test_msas/strict/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -strictplus > test_msas/strictplus/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -automated1 > test_msas/automated1/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -nogaps > test_msas/nogaps/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -noallgaps > test_msas/noallgaps/example.038.AA.bctoNOG.ENOG41099Y4.fasta +./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -gappyout > test_msas/gappyout/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -strict > test_msas/strict/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -strictplus > test_msas/strictplus/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -automated1 > test_msas/automated1/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -nogaps > test_msas/nogaps/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -noallgaps > test_msas/noallgaps/example.039.AA.bctoNOG.ENOG41099YD.fasta +./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -gappyout > test_msas/gappyout/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -strict > test_msas/strict/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -strictplus > test_msas/strictplus/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -automated1 > test_msas/automated1/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -nogaps > test_msas/nogaps/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -noallgaps > test_msas/noallgaps/example.040.AA.bctoNOG.ENOG4109A32.fasta +./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -gappyout > test_msas/gappyout/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -strict > test_msas/strict/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -strictplus > test_msas/strictplus/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -automated1 > test_msas/automated1/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -nogaps > test_msas/nogaps/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -noallgaps > test_msas/noallgaps/example.041.AA.bctoNOG.ENOG4109A5T.fasta +./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -gappyout > test_msas/gappyout/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -strict > test_msas/strict/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -strictplus > test_msas/strictplus/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -automated1 > test_msas/automated1/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -nogaps > test_msas/nogaps/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -noallgaps > test_msas/noallgaps/example.042.AA.bctoNOG.ENOG4109A9M.fasta +./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -gappyout > test_msas/gappyout/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -strict > test_msas/strict/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -strictplus > test_msas/strictplus/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -automated1 > test_msas/automated1/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -nogaps > test_msas/nogaps/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -noallgaps > test_msas/noallgaps/example.043.AA.bctoNOG.ENOG4109ADN.fasta +./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -gappyout > test_msas/gappyout/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -strict > test_msas/strict/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -strictplus > test_msas/strictplus/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -automated1 > test_msas/automated1/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -nogaps > test_msas/nogaps/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -noallgaps > test_msas/noallgaps/example.044.AA.bctoNOG.ENOG4109AED.fasta +./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -gappyout > test_msas/gappyout/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -strict > test_msas/strict/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -strictplus > test_msas/strictplus/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -automated1 > test_msas/automated1/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -nogaps > test_msas/nogaps/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -noallgaps > test_msas/noallgaps/example.045.AA.bctoNOG.ENOG4109AGT.fasta +./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -gappyout > test_msas/gappyout/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -strict > test_msas/strict/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -strictplus > test_msas/strictplus/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -automated1 > test_msas/automated1/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -nogaps > test_msas/nogaps/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -noallgaps > test_msas/noallgaps/example.046.AA.bctoNOG.ENOG4109AGW.fasta +./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -gappyout > test_msas/gappyout/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -strict > test_msas/strict/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -strictplus > test_msas/strictplus/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -automated1 > test_msas/automated1/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -nogaps > test_msas/nogaps/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -noallgaps > test_msas/noallgaps/example.047.AA.bctoNOG.ENOG4109AIC.fasta +./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -gappyout > test_msas/gappyout/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strict > test_msas/strict/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strictplus > test_msas/strictplus/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -automated1 > test_msas/automated1/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -nogaps > test_msas/nogaps/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -noallgaps > test_msas/noallgaps/example.048.AA.bctoNOG.ENOG4109AJ3.fasta +./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -gappyout > test_msas/gappyout/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -strict > test_msas/strict/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -strictplus > test_msas/strictplus/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -automated1 > test_msas/automated1/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -nogaps > test_msas/nogaps/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -noallgaps > test_msas/noallgaps/example.049.AA.bctoNOG.ENOG4109AY5.fasta +./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -gappyout > test_msas/gappyout/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strict > test_msas/strict/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strictplus > test_msas/strictplus/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -automated1 > test_msas/automated1/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -nogaps > test_msas/nogaps/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -noallgaps > test_msas/noallgaps/example.050.AA.bctoNOG.ENOG4109B8Z.fasta +./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -gappyout > test_msas/gappyout/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strict > test_msas/strict/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strictplus > test_msas/strictplus/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -automated1 > test_msas/automated1/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -nogaps > test_msas/nogaps/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -noallgaps > test_msas/noallgaps/example.051.AA.bctoNOG.ENOG4109BCJ.fasta +./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -gappyout > test_msas/gappyout/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -strict > test_msas/strict/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -strictplus > test_msas/strictplus/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -automated1 > test_msas/automated1/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -nogaps > test_msas/nogaps/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -noallgaps > test_msas/noallgaps/example.052.AA.bctoNOG.ENOG4109CTU.fasta +./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -gappyout > test_msas/gappyout/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -strict > test_msas/strict/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -strictplus > test_msas/strictplus/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -automated1 > test_msas/automated1/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -nogaps > test_msas/nogaps/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -noallgaps > test_msas/noallgaps/example.053.AA.bctoNOG.ENOG4109CVC.fasta +./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -gappyout > test_msas/gappyout/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -strict > test_msas/strict/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -strictplus > test_msas/strictplus/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -automated1 > test_msas/automated1/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -nogaps > test_msas/nogaps/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -noallgaps > test_msas/noallgaps/example.054.AA.bctoNOG.ENOG4109FIT.fasta +./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -gappyout > test_msas/gappyout/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -strict > test_msas/strict/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -strictplus > test_msas/strictplus/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -automated1 > test_msas/automated1/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -nogaps > test_msas/nogaps/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -noallgaps > test_msas/noallgaps/example.055.AA.bctoNOG.ENOG4109GY9.fasta +./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -gappyout > test_msas/gappyout/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strict > test_msas/strict/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strictplus > test_msas/strictplus/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -automated1 > test_msas/automated1/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -nogaps > test_msas/nogaps/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -noallgaps > test_msas/noallgaps/example.056.AA.bctoNOG.ENOG4109IPJ.fasta +./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -gappyout > test_msas/gappyout/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strict > test_msas/strict/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strictplus > test_msas/strictplus/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -automated1 > test_msas/automated1/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -nogaps > test_msas/nogaps/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -noallgaps > test_msas/noallgaps/example.057.AA.bctoNOG.ENOG4109SZ2.fasta +./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -gappyout > test_msas/gappyout/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -strict > test_msas/strict/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -strictplus > test_msas/strictplus/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -automated1 > test_msas/automated1/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -nogaps > test_msas/nogaps/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -noallgaps > test_msas/noallgaps/example.058.AA.strNOG.ENOG411BBR6.fasta +./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -gappyout > test_msas/gappyout/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -strict > test_msas/strict/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -strictplus > test_msas/strictplus/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -automated1 > test_msas/automated1/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -nogaps > test_msas/nogaps/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -noallgaps > test_msas/noallgaps/example.059.AA.strNOG.ENOG411BBRR.fasta +./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -gappyout > test_msas/gappyout/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -strict > test_msas/strict/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -strictplus > test_msas/strictplus/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -automated1 > test_msas/automated1/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -nogaps > test_msas/nogaps/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -noallgaps > test_msas/noallgaps/example.060.AA.strNOG.ENOG411BBWK.fasta +./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -gappyout > test_msas/gappyout/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -strict > test_msas/strict/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -strictplus > test_msas/strictplus/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -automated1 > test_msas/automated1/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -nogaps > test_msas/nogaps/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -noallgaps > test_msas/noallgaps/example.061.AA.strNOG.ENOG411BCDZ.fasta +./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -gappyout > test_msas/gappyout/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -strict > test_msas/strict/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -strictplus > test_msas/strictplus/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -automated1 > test_msas/automated1/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -nogaps > test_msas/nogaps/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -noallgaps > test_msas/noallgaps/example.062.AA.strNOG.ENOG411BCX3.fasta +./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -gappyout > test_msas/gappyout/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -strict > test_msas/strict/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -strictplus > test_msas/strictplus/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -automated1 > test_msas/automated1/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -nogaps > test_msas/nogaps/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -noallgaps > test_msas/noallgaps/example.063.AA.strNOG.ENOG411BDBU.fasta +./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -gappyout > test_msas/gappyout/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -strict > test_msas/strict/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -strictplus > test_msas/strictplus/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -automated1 > test_msas/automated1/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -nogaps > test_msas/nogaps/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -noallgaps > test_msas/noallgaps/example.064.AA.strNOG.ENOG411BDKC.fasta +./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -gappyout > test_msas/gappyout/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -strict > test_msas/strict/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -strictplus > test_msas/strictplus/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -automated1 > test_msas/automated1/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -nogaps > test_msas/nogaps/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -noallgaps > test_msas/noallgaps/example.065.AA.strNOG.ENOG411BDSZ.fasta +./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -gappyout > test_msas/gappyout/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -strict > test_msas/strict/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -strictplus > test_msas/strictplus/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -automated1 > test_msas/automated1/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -nogaps > test_msas/nogaps/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -noallgaps > test_msas/noallgaps/example.066.AA.strNOG.ENOG411BDUE.fasta +./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -gappyout > test_msas/gappyout/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -strict > test_msas/strict/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -strictplus > test_msas/strictplus/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -automated1 > test_msas/automated1/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -nogaps > test_msas/nogaps/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -noallgaps > test_msas/noallgaps/example.067.AA.strNOG.ENOG411BDX3.fasta +./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -gappyout > test_msas/gappyout/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -strict > test_msas/strict/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -strictplus > test_msas/strictplus/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -automated1 > test_msas/automated1/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -nogaps > test_msas/nogaps/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -noallgaps > test_msas/noallgaps/example.068.AA.strNOG.ENOG411BE45.fasta +./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -gappyout > test_msas/gappyout/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -strict > test_msas/strict/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -strictplus > test_msas/strictplus/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -automated1 > test_msas/automated1/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -nogaps > test_msas/nogaps/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -noallgaps > test_msas/noallgaps/example.069.AA.strNOG.ENOG411BE8B.fasta +./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -gappyout > test_msas/gappyout/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -strict > test_msas/strict/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -strictplus > test_msas/strictplus/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -automated1 > test_msas/automated1/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -nogaps > test_msas/nogaps/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -noallgaps > test_msas/noallgaps/example.070.AA.strNOG.ENOG411BEUV.fasta +./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -gappyout > test_msas/gappyout/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -strict > test_msas/strict/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -strictplus > test_msas/strictplus/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -automated1 > test_msas/automated1/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -nogaps > test_msas/nogaps/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -noallgaps > test_msas/noallgaps/example.071.AA.strNOG.ENOG411BEZ0.fasta +./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -gappyout > test_msas/gappyout/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -strict > test_msas/strict/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -strictplus > test_msas/strictplus/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -automated1 > test_msas/automated1/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -nogaps > test_msas/nogaps/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -noallgaps > test_msas/noallgaps/example.072.AA.strNOG.ENOG411BF1S.fasta +./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -gappyout > test_msas/gappyout/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -strict > test_msas/strict/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -strictplus > test_msas/strictplus/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -automated1 > test_msas/automated1/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -nogaps > test_msas/nogaps/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -noallgaps > test_msas/noallgaps/example.073.AA.strNOG.ENOG411BFCW.fasta +./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -gappyout > test_msas/gappyout/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -strict > test_msas/strict/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -strictplus > test_msas/strictplus/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -automated1 > test_msas/automated1/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -nogaps > test_msas/nogaps/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -noallgaps > test_msas/noallgaps/example.074.AA.strNOG.ENOG411BFPF.fasta +./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -gappyout > test_msas/gappyout/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -strict > test_msas/strict/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -strictplus > test_msas/strictplus/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -automated1 > test_msas/automated1/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -nogaps > test_msas/nogaps/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -noallgaps > test_msas/noallgaps/example.075.AA.strNOG.ENOG411BFQS.fasta +./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -gappyout > test_msas/gappyout/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -strict > test_msas/strict/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -strictplus > test_msas/strictplus/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -automated1 > test_msas/automated1/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -nogaps > test_msas/nogaps/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -noallgaps > test_msas/noallgaps/example.076.AA.strNOG.ENOG411BH75.fasta +./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -gappyout > test_msas/gappyout/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -strict > test_msas/strict/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -strictplus > test_msas/strictplus/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -automated1 > test_msas/automated1/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -nogaps > test_msas/nogaps/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -noallgaps > test_msas/noallgaps/example.077.AA.strNOG.ENOG411BH79.fasta +./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -gappyout > test_msas/gappyout/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -strict > test_msas/strict/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -strictplus > test_msas/strictplus/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -automated1 > test_msas/automated1/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -nogaps > test_msas/nogaps/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -noallgaps > test_msas/noallgaps/example.078.AA.strNOG.ENOG411BH99.fasta +./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -gappyout > test_msas/gappyout/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -strict > test_msas/strict/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -strictplus > test_msas/strictplus/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -automated1 > test_msas/automated1/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -nogaps > test_msas/nogaps/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -noallgaps > test_msas/noallgaps/example.079.AA.strNOG.ENOG411BJDC.fasta +./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -gappyout > test_msas/gappyout/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -strict > test_msas/strict/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -strictplus > test_msas/strictplus/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -automated1 > test_msas/automated1/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -nogaps > test_msas/nogaps/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -noallgaps > test_msas/noallgaps/example.080.AA.strNOG.ENOG411BJIF.fasta +./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -gappyout > test_msas/gappyout/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -strict > test_msas/strict/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -strictplus > test_msas/strictplus/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -automated1 > test_msas/automated1/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -nogaps > test_msas/nogaps/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -noallgaps > test_msas/noallgaps/example.081.AA.strNOG.ENOG411BK9X.fasta +./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -gappyout > test_msas/gappyout/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -strict > test_msas/strict/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -strictplus > test_msas/strictplus/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -automated1 > test_msas/automated1/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -nogaps > test_msas/nogaps/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -noallgaps > test_msas/noallgaps/example.082.AA.strNOG.ENOG411BKC5.fasta +./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -gappyout > test_msas/gappyout/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -strict > test_msas/strict/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -strictplus > test_msas/strictplus/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -automated1 > test_msas/automated1/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -nogaps > test_msas/nogaps/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -noallgaps > test_msas/noallgaps/example.083.AA.strNOG.ENOG411BMKC.fasta +./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -gappyout > test_msas/gappyout/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -strict > test_msas/strict/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -strictplus > test_msas/strictplus/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -automated1 > test_msas/automated1/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -nogaps > test_msas/nogaps/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -noallgaps > test_msas/noallgaps/example.084.AA.strNOG.ENOG411BNP9.fasta +./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -gappyout > test_msas/gappyout/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -strict > test_msas/strict/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -strictplus > test_msas/strictplus/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -automated1 > test_msas/automated1/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -nogaps > test_msas/nogaps/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -noallgaps > test_msas/noallgaps/example.085.AA.strNOG.ENOG411BQTJ.fasta +./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -gappyout > test_msas/gappyout/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -strict > test_msas/strict/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -strictplus > test_msas/strictplus/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -automated1 > test_msas/automated1/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -nogaps > test_msas/nogaps/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -noallgaps > test_msas/noallgaps/example.086.AA.strNOG.ENOG411BR1D.fasta +./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -gappyout > test_msas/gappyout/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -strict > test_msas/strict/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -strictplus > test_msas/strictplus/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -automated1 > test_msas/automated1/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -nogaps > test_msas/nogaps/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -noallgaps > test_msas/noallgaps/example.087.AA.strNOG.ENOG411BRCH.fasta +./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -gappyout > test_msas/gappyout/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -strict > test_msas/strict/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -strictplus > test_msas/strictplus/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -automated1 > test_msas/automated1/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -nogaps > test_msas/nogaps/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -noallgaps > test_msas/noallgaps/example.088.AA.strNOG.ENOG411BSXF.fasta +./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -gappyout > test_msas/gappyout/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -strict > test_msas/strict/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -strictplus > test_msas/strictplus/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -automated1 > test_msas/automated1/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -nogaps > test_msas/nogaps/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -noallgaps > test_msas/noallgaps/example.089.AA.strNOG.ENOG411BV9B.fasta +./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -gappyout > test_msas/gappyout/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -strict > test_msas/strict/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -strictplus > test_msas/strictplus/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -automated1 > test_msas/automated1/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -nogaps > test_msas/nogaps/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -noallgaps > test_msas/noallgaps/example.090.AA.strNOG.ENOG411BVKR.fasta +./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -gappyout > test_msas/gappyout/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -strict > test_msas/strict/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -strictplus > test_msas/strictplus/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -automated1 > test_msas/automated1/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -nogaps > test_msas/nogaps/example.091.AA.strNOG.ENOG411BWBU.fasta +./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -noallgaps > test_msas/noallgaps/example.091.AA.strNOG.ENOG411BWBU.fasta From e99735bed53dbd1547a86b84216a104ab3a62c2b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 10:22:41 +0200 Subject: [PATCH 47/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 1f9a8f15a..30096e3de 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched. +Temporary file to force Github Actions workflow to be launched From c0c8416852d8fa0eb7ace29a9f1be50356cf34ae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 10:30:59 +0200 Subject: [PATCH 48/61] Fix executable path --- scripts/generate_trimmed_msas.ps1 | 1008 ++++++++++++++--------------- 1 file changed, 504 insertions(+), 504 deletions(-) diff --git a/scripts/generate_trimmed_msas.ps1 b/scripts/generate_trimmed_msas.ps1 index be61da6f6..70e5945f6 100644 --- a/scripts/generate_trimmed_msas.ps1 +++ b/scripts/generate_trimmed_msas.ps1 @@ -8,507 +8,507 @@ New-Item -ItemType Directory -Path "test_msas\nogaps" New-Item -ItemType Directory -Path "test_msas\noallgaps" # Run trimal commands -.\trimal.exe -in dataset\example.004.AA.fasta -gappyout > test_msas\gappyout\example.004.AA.fasta -.\trimal.exe -in dataset\example.004.AA.fasta -strict > test_msas\strict\example.004.AA.fasta -.\trimal.exe -in dataset\example.004.AA.fasta -strictplus > test_msas\strictplus\example.004.AA.fasta -.\trimal.exe -in dataset\example.004.AA.fasta -automated1 > test_msas\automated1\example.004.AA.fasta -.\trimal.exe -in dataset\example.004.AA.fasta -nogaps > test_msas\nogaps\example.004.AA.fasta -.\trimal.exe -in dataset\example.004.AA.fasta -noallgaps > test_msas\noallgaps\example.004.AA.fasta -.\trimal.exe -in dataset\example.005.AA.fasta -gappyout > test_msas\gappyout\example.005.AA.fasta -.\trimal.exe -in dataset\example.005.AA.fasta -strict > test_msas\strict\example.005.AA.fasta -.\trimal.exe -in dataset\example.005.AA.fasta -strictplus > test_msas\strictplus\example.005.AA.fasta -.\trimal.exe -in dataset\example.005.AA.fasta -automated1 > test_msas\automated1\example.005.AA.fasta -.\trimal.exe -in dataset\example.005.AA.fasta -nogaps > test_msas\nogaps\example.005.AA.fasta -.\trimal.exe -in dataset\example.005.AA.fasta -noallgaps > test_msas\noallgaps\example.005.AA.fasta -.\trimal.exe -in dataset\example.007.AA.fasta -gappyout > test_msas\gappyout\example.007.AA.fasta -.\trimal.exe -in dataset\example.007.AA.fasta -strict > test_msas\strict\example.007.AA.fasta -.\trimal.exe -in dataset\example.007.AA.fasta -strictplus > test_msas\strictplus\example.007.AA.fasta -.\trimal.exe -in dataset\example.007.AA.fasta -automated1 > test_msas\automated1\example.007.AA.fasta -.\trimal.exe -in dataset\example.007.AA.fasta -nogaps > test_msas\nogaps\example.007.AA.fasta -.\trimal.exe -in dataset\example.007.AA.fasta -noallgaps > test_msas\noallgaps\example.007.AA.fasta -.\trimal.exe -in dataset\example.009.AA.fasta -gappyout > test_msas\gappyout\example.009.AA.fasta -.\trimal.exe -in dataset\example.009.AA.fasta -strict > test_msas\strict\example.009.AA.fasta -.\trimal.exe -in dataset\example.009.AA.fasta -strictplus > test_msas\strictplus\example.009.AA.fasta -.\trimal.exe -in dataset\example.009.AA.fasta -automated1 > test_msas\automated1\example.009.AA.fasta -.\trimal.exe -in dataset\example.009.AA.fasta -nogaps > test_msas\nogaps\example.009.AA.fasta -.\trimal.exe -in dataset\example.009.AA.fasta -noallgaps > test_msas\noallgaps\example.009.AA.fasta -.\trimal.exe -in dataset\example.010.AA.fasta -gappyout > test_msas\gappyout\example.010.AA.fasta -.\trimal.exe -in dataset\example.010.AA.fasta -strict > test_msas\strict\example.010.AA.fasta -.\trimal.exe -in dataset\example.010.AA.fasta -strictplus > test_msas\strictplus\example.010.AA.fasta -.\trimal.exe -in dataset\example.010.AA.fasta -automated1 > test_msas\automated1\example.010.AA.fasta -.\trimal.exe -in dataset\example.010.AA.fasta -nogaps > test_msas\nogaps\example.010.AA.fasta -.\trimal.exe -in dataset\example.010.AA.fasta -noallgaps > test_msas\noallgaps\example.010.AA.fasta -.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -gappyout > test_msas\gappyout\example.011.AA.YKL197C.fasta -.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -strict > test_msas\strict\example.011.AA.YKL197C.fasta -.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -strictplus > test_msas\strictplus\example.011.AA.YKL197C.fasta -.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -automated1 > test_msas\automated1\example.011.AA.YKL197C.fasta -.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -nogaps > test_msas\nogaps\example.011.AA.YKL197C.fasta -.\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -noallgaps > test_msas\noallgaps\example.011.AA.YKL197C.fasta -.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -gappyout > test_msas\gappyout\example.014.AA.EggNOG.COG0591.fasta -.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -strict > test_msas\strict\example.014.AA.EggNOG.COG0591.fasta -.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -strictplus > test_msas\strictplus\example.014.AA.EggNOG.COG0591.fasta -.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -automated1 > test_msas\automated1\example.014.AA.EggNOG.COG0591.fasta -.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -nogaps > test_msas\nogaps\example.014.AA.EggNOG.COG0591.fasta -.\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -noallgaps > test_msas\noallgaps\example.014.AA.EggNOG.COG0591.fasta -.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -gappyout > test_msas\gappyout\example.015.AA.bctoNOG.ENOG41099F3.fasta -.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -strict > test_msas\strict\example.015.AA.bctoNOG.ENOG41099F3.fasta -.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -strictplus > test_msas\strictplus\example.015.AA.bctoNOG.ENOG41099F3.fasta -.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -automated1 > test_msas\automated1\example.015.AA.bctoNOG.ENOG41099F3.fasta -.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -nogaps > test_msas\nogaps\example.015.AA.bctoNOG.ENOG41099F3.fasta -.\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -noallgaps > test_msas\noallgaps\example.015.AA.bctoNOG.ENOG41099F3.fasta -.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -gappyout > test_msas\gappyout\example.016.AA.bctoNOG.ENOG41099FB.fasta -.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -strict > test_msas\strict\example.016.AA.bctoNOG.ENOG41099FB.fasta -.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -strictplus > test_msas\strictplus\example.016.AA.bctoNOG.ENOG41099FB.fasta -.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -automated1 > test_msas\automated1\example.016.AA.bctoNOG.ENOG41099FB.fasta -.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -nogaps > test_msas\nogaps\example.016.AA.bctoNOG.ENOG41099FB.fasta -.\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -noallgaps > test_msas\noallgaps\example.016.AA.bctoNOG.ENOG41099FB.fasta -.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -gappyout > test_msas\gappyout\example.017.AA.bctoNOG.ENOG41099FJ.fasta -.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -strict > test_msas\strict\example.017.AA.bctoNOG.ENOG41099FJ.fasta -.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -strictplus > test_msas\strictplus\example.017.AA.bctoNOG.ENOG41099FJ.fasta -.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -automated1 > test_msas\automated1\example.017.AA.bctoNOG.ENOG41099FJ.fasta -.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -nogaps > test_msas\nogaps\example.017.AA.bctoNOG.ENOG41099FJ.fasta -.\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -noallgaps > test_msas\noallgaps\example.017.AA.bctoNOG.ENOG41099FJ.fasta -.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -gappyout > test_msas\gappyout\example.018.AA.bctoNOG.ENOG41099FV.fasta -.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -strict > test_msas\strict\example.018.AA.bctoNOG.ENOG41099FV.fasta -.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -strictplus > test_msas\strictplus\example.018.AA.bctoNOG.ENOG41099FV.fasta -.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -automated1 > test_msas\automated1\example.018.AA.bctoNOG.ENOG41099FV.fasta -.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -nogaps > test_msas\nogaps\example.018.AA.bctoNOG.ENOG41099FV.fasta -.\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -noallgaps > test_msas\noallgaps\example.018.AA.bctoNOG.ENOG41099FV.fasta -.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -gappyout > test_msas\gappyout\example.019.AA.bctoNOG.ENOG41099HI.fasta -.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -strict > test_msas\strict\example.019.AA.bctoNOG.ENOG41099HI.fasta -.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -strictplus > test_msas\strictplus\example.019.AA.bctoNOG.ENOG41099HI.fasta -.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -automated1 > test_msas\automated1\example.019.AA.bctoNOG.ENOG41099HI.fasta -.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -nogaps > test_msas\nogaps\example.019.AA.bctoNOG.ENOG41099HI.fasta -.\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -noallgaps > test_msas\noallgaps\example.019.AA.bctoNOG.ENOG41099HI.fasta -.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -gappyout > test_msas\gappyout\example.020.AA.bctoNOG.ENOG41099HN.fasta -.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -strict > test_msas\strict\example.020.AA.bctoNOG.ENOG41099HN.fasta -.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -strictplus > test_msas\strictplus\example.020.AA.bctoNOG.ENOG41099HN.fasta -.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -automated1 > test_msas\automated1\example.020.AA.bctoNOG.ENOG41099HN.fasta -.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -nogaps > test_msas\nogaps\example.020.AA.bctoNOG.ENOG41099HN.fasta -.\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -noallgaps > test_msas\noallgaps\example.020.AA.bctoNOG.ENOG41099HN.fasta -.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -gappyout > test_msas\gappyout\example.021.AA.bctoNOG.ENOG41099I5.fasta -.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -strict > test_msas\strict\example.021.AA.bctoNOG.ENOG41099I5.fasta -.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -strictplus > test_msas\strictplus\example.021.AA.bctoNOG.ENOG41099I5.fasta -.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -automated1 > test_msas\automated1\example.021.AA.bctoNOG.ENOG41099I5.fasta -.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -nogaps > test_msas\nogaps\example.021.AA.bctoNOG.ENOG41099I5.fasta -.\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -noallgaps > test_msas\noallgaps\example.021.AA.bctoNOG.ENOG41099I5.fasta -.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -gappyout > test_msas\gappyout\example.022.AA.bctoNOG.ENOG41099IZ.fasta -.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -strict > test_msas\strict\example.022.AA.bctoNOG.ENOG41099IZ.fasta -.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -strictplus > test_msas\strictplus\example.022.AA.bctoNOG.ENOG41099IZ.fasta -.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -automated1 > test_msas\automated1\example.022.AA.bctoNOG.ENOG41099IZ.fasta -.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -nogaps > test_msas\nogaps\example.022.AA.bctoNOG.ENOG41099IZ.fasta -.\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -noallgaps > test_msas\noallgaps\example.022.AA.bctoNOG.ENOG41099IZ.fasta -.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -gappyout > test_msas\gappyout\example.023.AA.bctoNOG.ENOG41099K3.fasta -.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -strict > test_msas\strict\example.023.AA.bctoNOG.ENOG41099K3.fasta -.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -strictplus > test_msas\strictplus\example.023.AA.bctoNOG.ENOG41099K3.fasta -.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -automated1 > test_msas\automated1\example.023.AA.bctoNOG.ENOG41099K3.fasta -.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -nogaps > test_msas\nogaps\example.023.AA.bctoNOG.ENOG41099K3.fasta -.\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -noallgaps > test_msas\noallgaps\example.023.AA.bctoNOG.ENOG41099K3.fasta -.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -gappyout > test_msas\gappyout\example.024.AA.bctoNOG.ENOG41099KM.fasta -.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -strict > test_msas\strict\example.024.AA.bctoNOG.ENOG41099KM.fasta -.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -strictplus > test_msas\strictplus\example.024.AA.bctoNOG.ENOG41099KM.fasta -.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -automated1 > test_msas\automated1\example.024.AA.bctoNOG.ENOG41099KM.fasta -.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -nogaps > test_msas\nogaps\example.024.AA.bctoNOG.ENOG41099KM.fasta -.\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -noallgaps > test_msas\noallgaps\example.024.AA.bctoNOG.ENOG41099KM.fasta -.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -gappyout > test_msas\gappyout\example.025.AA.bctoNOG.ENOG41099KP.fasta -.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -strict > test_msas\strict\example.025.AA.bctoNOG.ENOG41099KP.fasta -.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -strictplus > test_msas\strictplus\example.025.AA.bctoNOG.ENOG41099KP.fasta -.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -automated1 > test_msas\automated1\example.025.AA.bctoNOG.ENOG41099KP.fasta -.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -nogaps > test_msas\nogaps\example.025.AA.bctoNOG.ENOG41099KP.fasta -.\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -noallgaps > test_msas\noallgaps\example.025.AA.bctoNOG.ENOG41099KP.fasta -.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -gappyout > test_msas\gappyout\example.026.AA.bctoNOG.ENOG41099MV.fasta -.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -strict > test_msas\strict\example.026.AA.bctoNOG.ENOG41099MV.fasta -.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -strictplus > test_msas\strictplus\example.026.AA.bctoNOG.ENOG41099MV.fasta -.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -automated1 > test_msas\automated1\example.026.AA.bctoNOG.ENOG41099MV.fasta -.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -nogaps > test_msas\nogaps\example.026.AA.bctoNOG.ENOG41099MV.fasta -.\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -noallgaps > test_msas\noallgaps\example.026.AA.bctoNOG.ENOG41099MV.fasta -.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -gappyout > test_msas\gappyout\example.027.AA.bctoNOG.ENOG41099NY.fasta -.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -strict > test_msas\strict\example.027.AA.bctoNOG.ENOG41099NY.fasta -.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -strictplus > test_msas\strictplus\example.027.AA.bctoNOG.ENOG41099NY.fasta -.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -automated1 > test_msas\automated1\example.027.AA.bctoNOG.ENOG41099NY.fasta -.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -nogaps > test_msas\nogaps\example.027.AA.bctoNOG.ENOG41099NY.fasta -.\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -noallgaps > test_msas\noallgaps\example.027.AA.bctoNOG.ENOG41099NY.fasta -.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -gappyout > test_msas\gappyout\example.028.AA.bctoNOG.ENOG41099PA.fasta -.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -strict > test_msas\strict\example.028.AA.bctoNOG.ENOG41099PA.fasta -.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -strictplus > test_msas\strictplus\example.028.AA.bctoNOG.ENOG41099PA.fasta -.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -automated1 > test_msas\automated1\example.028.AA.bctoNOG.ENOG41099PA.fasta -.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -nogaps > test_msas\nogaps\example.028.AA.bctoNOG.ENOG41099PA.fasta -.\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -noallgaps > test_msas\noallgaps\example.028.AA.bctoNOG.ENOG41099PA.fasta -.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -gappyout > test_msas\gappyout\example.029.AA.bctoNOG.ENOG41099Q3.fasta -.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -strict > test_msas\strict\example.029.AA.bctoNOG.ENOG41099Q3.fasta -.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -strictplus > test_msas\strictplus\example.029.AA.bctoNOG.ENOG41099Q3.fasta -.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -automated1 > test_msas\automated1\example.029.AA.bctoNOG.ENOG41099Q3.fasta -.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -nogaps > test_msas\nogaps\example.029.AA.bctoNOG.ENOG41099Q3.fasta -.\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -noallgaps > test_msas\noallgaps\example.029.AA.bctoNOG.ENOG41099Q3.fasta -.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -gappyout > test_msas\gappyout\example.030.AA.bctoNOG.ENOG41099RG.fasta -.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -strict > test_msas\strict\example.030.AA.bctoNOG.ENOG41099RG.fasta -.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -strictplus > test_msas\strictplus\example.030.AA.bctoNOG.ENOG41099RG.fasta -.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -automated1 > test_msas\automated1\example.030.AA.bctoNOG.ENOG41099RG.fasta -.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -nogaps > test_msas\nogaps\example.030.AA.bctoNOG.ENOG41099RG.fasta -.\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -noallgaps > test_msas\noallgaps\example.030.AA.bctoNOG.ENOG41099RG.fasta -.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -gappyout > test_msas\gappyout\example.031.AA.bctoNOG.ENOG41099UK.fasta -.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -strict > test_msas\strict\example.031.AA.bctoNOG.ENOG41099UK.fasta -.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -strictplus > test_msas\strictplus\example.031.AA.bctoNOG.ENOG41099UK.fasta -.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -automated1 > test_msas\automated1\example.031.AA.bctoNOG.ENOG41099UK.fasta -.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -nogaps > test_msas\nogaps\example.031.AA.bctoNOG.ENOG41099UK.fasta -.\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -noallgaps > test_msas\noallgaps\example.031.AA.bctoNOG.ENOG41099UK.fasta -.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -gappyout > test_msas\gappyout\example.032.AA.bctoNOG.ENOG41099UW.fasta -.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -strict > test_msas\strict\example.032.AA.bctoNOG.ENOG41099UW.fasta -.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -strictplus > test_msas\strictplus\example.032.AA.bctoNOG.ENOG41099UW.fasta -.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -automated1 > test_msas\automated1\example.032.AA.bctoNOG.ENOG41099UW.fasta -.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -nogaps > test_msas\nogaps\example.032.AA.bctoNOG.ENOG41099UW.fasta -.\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -noallgaps > test_msas\noallgaps\example.032.AA.bctoNOG.ENOG41099UW.fasta -.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -gappyout > test_msas\gappyout\example.033.AA.bctoNOG.ENOG41099VK.fasta -.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -strict > test_msas\strict\example.033.AA.bctoNOG.ENOG41099VK.fasta -.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -strictplus > test_msas\strictplus\example.033.AA.bctoNOG.ENOG41099VK.fasta -.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -automated1 > test_msas\automated1\example.033.AA.bctoNOG.ENOG41099VK.fasta -.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -nogaps > test_msas\nogaps\example.033.AA.bctoNOG.ENOG41099VK.fasta -.\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -noallgaps > test_msas\noallgaps\example.033.AA.bctoNOG.ENOG41099VK.fasta -.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -gappyout > test_msas\gappyout\example.034.AA.bctoNOG.ENOG41099WA.fasta -.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -strict > test_msas\strict\example.034.AA.bctoNOG.ENOG41099WA.fasta -.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -strictplus > test_msas\strictplus\example.034.AA.bctoNOG.ENOG41099WA.fasta -.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -automated1 > test_msas\automated1\example.034.AA.bctoNOG.ENOG41099WA.fasta -.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -nogaps > test_msas\nogaps\example.034.AA.bctoNOG.ENOG41099WA.fasta -.\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -noallgaps > test_msas\noallgaps\example.034.AA.bctoNOG.ENOG41099WA.fasta -.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -gappyout > test_msas\gappyout\example.035.AA.bctoNOG.ENOG41099WF.fasta -.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -strict > test_msas\strict\example.035.AA.bctoNOG.ENOG41099WF.fasta -.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -strictplus > test_msas\strictplus\example.035.AA.bctoNOG.ENOG41099WF.fasta -.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -automated1 > test_msas\automated1\example.035.AA.bctoNOG.ENOG41099WF.fasta -.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -nogaps > test_msas\nogaps\example.035.AA.bctoNOG.ENOG41099WF.fasta -.\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -noallgaps > test_msas\noallgaps\example.035.AA.bctoNOG.ENOG41099WF.fasta -.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -gappyout > test_msas\gappyout\example.036.AA.bctoNOG.ENOG41099XJ.fasta -.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -strict > test_msas\strict\example.036.AA.bctoNOG.ENOG41099XJ.fasta -.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -strictplus > test_msas\strictplus\example.036.AA.bctoNOG.ENOG41099XJ.fasta -.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -automated1 > test_msas\automated1\example.036.AA.bctoNOG.ENOG41099XJ.fasta -.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -nogaps > test_msas\nogaps\example.036.AA.bctoNOG.ENOG41099XJ.fasta -.\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -noallgaps > test_msas\noallgaps\example.036.AA.bctoNOG.ENOG41099XJ.fasta -.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -gappyout > test_msas\gappyout\example.037.AA.bctoNOG.ENOG41099XP.fasta -.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -strict > test_msas\strict\example.037.AA.bctoNOG.ENOG41099XP.fasta -.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -strictplus > test_msas\strictplus\example.037.AA.bctoNOG.ENOG41099XP.fasta -.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -automated1 > test_msas\automated1\example.037.AA.bctoNOG.ENOG41099XP.fasta -.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -nogaps > test_msas\nogaps\example.037.AA.bctoNOG.ENOG41099XP.fasta -.\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -noallgaps > test_msas\noallgaps\example.037.AA.bctoNOG.ENOG41099XP.fasta -.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -gappyout > test_msas\gappyout\example.038.AA.bctoNOG.ENOG41099Y4.fasta -.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -strict > test_msas\strict\example.038.AA.bctoNOG.ENOG41099Y4.fasta -.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -strictplus > test_msas\strictplus\example.038.AA.bctoNOG.ENOG41099Y4.fasta -.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -automated1 > test_msas\automated1\example.038.AA.bctoNOG.ENOG41099Y4.fasta -.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -nogaps > test_msas\nogaps\example.038.AA.bctoNOG.ENOG41099Y4.fasta -.\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -noallgaps > test_msas\noallgaps\example.038.AA.bctoNOG.ENOG41099Y4.fasta -.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -gappyout > test_msas\gappyout\example.039.AA.bctoNOG.ENOG41099YD.fasta -.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -strict > test_msas\strict\example.039.AA.bctoNOG.ENOG41099YD.fasta -.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -strictplus > test_msas\strictplus\example.039.AA.bctoNOG.ENOG41099YD.fasta -.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -automated1 > test_msas\automated1\example.039.AA.bctoNOG.ENOG41099YD.fasta -.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -nogaps > test_msas\nogaps\example.039.AA.bctoNOG.ENOG41099YD.fasta -.\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -noallgaps > test_msas\noallgaps\example.039.AA.bctoNOG.ENOG41099YD.fasta -.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -gappyout > test_msas\gappyout\example.040.AA.bctoNOG.ENOG4109A32.fasta -.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -strict > test_msas\strict\example.040.AA.bctoNOG.ENOG4109A32.fasta -.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -strictplus > test_msas\strictplus\example.040.AA.bctoNOG.ENOG4109A32.fasta -.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -automated1 > test_msas\automated1\example.040.AA.bctoNOG.ENOG4109A32.fasta -.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -nogaps > test_msas\nogaps\example.040.AA.bctoNOG.ENOG4109A32.fasta -.\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -noallgaps > test_msas\noallgaps\example.040.AA.bctoNOG.ENOG4109A32.fasta -.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -gappyout > test_msas\gappyout\example.041.AA.bctoNOG.ENOG4109A5T.fasta -.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -strict > test_msas\strict\example.041.AA.bctoNOG.ENOG4109A5T.fasta -.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -strictplus > test_msas\strictplus\example.041.AA.bctoNOG.ENOG4109A5T.fasta -.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -automated1 > test_msas\automated1\example.041.AA.bctoNOG.ENOG4109A5T.fasta -.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -nogaps > test_msas\nogaps\example.041.AA.bctoNOG.ENOG4109A5T.fasta -.\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -noallgaps > test_msas\noallgaps\example.041.AA.bctoNOG.ENOG4109A5T.fasta -.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -gappyout > test_msas\gappyout\example.042.AA.bctoNOG.ENOG4109A9M.fasta -.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -strict > test_msas\strict\example.042.AA.bctoNOG.ENOG4109A9M.fasta -.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -strictplus > test_msas\strictplus\example.042.AA.bctoNOG.ENOG4109A9M.fasta -.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -automated1 > test_msas\automated1\example.042.AA.bctoNOG.ENOG4109A9M.fasta -.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -nogaps > test_msas\nogaps\example.042.AA.bctoNOG.ENOG4109A9M.fasta -.\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -noallgaps > test_msas\noallgaps\example.042.AA.bctoNOG.ENOG4109A9M.fasta -.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -gappyout > test_msas\gappyout\example.043.AA.bctoNOG.ENOG4109ADN.fasta -.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -strict > test_msas\strict\example.043.AA.bctoNOG.ENOG4109ADN.fasta -.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -strictplus > test_msas\strictplus\example.043.AA.bctoNOG.ENOG4109ADN.fasta -.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -automated1 > test_msas\automated1\example.043.AA.bctoNOG.ENOG4109ADN.fasta -.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -nogaps > test_msas\nogaps\example.043.AA.bctoNOG.ENOG4109ADN.fasta -.\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -noallgaps > test_msas\noallgaps\example.043.AA.bctoNOG.ENOG4109ADN.fasta -.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -gappyout > test_msas\gappyout\example.044.AA.bctoNOG.ENOG4109AED.fasta -.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -strict > test_msas\strict\example.044.AA.bctoNOG.ENOG4109AED.fasta -.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -strictplus > test_msas\strictplus\example.044.AA.bctoNOG.ENOG4109AED.fasta -.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -automated1 > test_msas\automated1\example.044.AA.bctoNOG.ENOG4109AED.fasta -.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -nogaps > test_msas\nogaps\example.044.AA.bctoNOG.ENOG4109AED.fasta -.\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -noallgaps > test_msas\noallgaps\example.044.AA.bctoNOG.ENOG4109AED.fasta -.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -gappyout > test_msas\gappyout\example.045.AA.bctoNOG.ENOG4109AGT.fasta -.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -strict > test_msas\strict\example.045.AA.bctoNOG.ENOG4109AGT.fasta -.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -strictplus > test_msas\strictplus\example.045.AA.bctoNOG.ENOG4109AGT.fasta -.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -automated1 > test_msas\automated1\example.045.AA.bctoNOG.ENOG4109AGT.fasta -.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -nogaps > test_msas\nogaps\example.045.AA.bctoNOG.ENOG4109AGT.fasta -.\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -noallgaps > test_msas\noallgaps\example.045.AA.bctoNOG.ENOG4109AGT.fasta -.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -gappyout > test_msas\gappyout\example.046.AA.bctoNOG.ENOG4109AGW.fasta -.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -strict > test_msas\strict\example.046.AA.bctoNOG.ENOG4109AGW.fasta -.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -strictplus > test_msas\strictplus\example.046.AA.bctoNOG.ENOG4109AGW.fasta -.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -automated1 > test_msas\automated1\example.046.AA.bctoNOG.ENOG4109AGW.fasta -.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -nogaps > test_msas\nogaps\example.046.AA.bctoNOG.ENOG4109AGW.fasta -.\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -noallgaps > test_msas\noallgaps\example.046.AA.bctoNOG.ENOG4109AGW.fasta -.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -gappyout > test_msas\gappyout\example.047.AA.bctoNOG.ENOG4109AIC.fasta -.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -strict > test_msas\strict\example.047.AA.bctoNOG.ENOG4109AIC.fasta -.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -strictplus > test_msas\strictplus\example.047.AA.bctoNOG.ENOG4109AIC.fasta -.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -automated1 > test_msas\automated1\example.047.AA.bctoNOG.ENOG4109AIC.fasta -.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -nogaps > test_msas\nogaps\example.047.AA.bctoNOG.ENOG4109AIC.fasta -.\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -noallgaps > test_msas\noallgaps\example.047.AA.bctoNOG.ENOG4109AIC.fasta -.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -gappyout > test_msas\gappyout\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strict > test_msas\strict\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strictplus > test_msas\strictplus\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -automated1 > test_msas\automated1\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -nogaps > test_msas\nogaps\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -.\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -noallgaps > test_msas\noallgaps\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -gappyout > test_msas\gappyout\example.049.AA.bctoNOG.ENOG4109AY5.fasta -.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -strict > test_msas\strict\example.049.AA.bctoNOG.ENOG4109AY5.fasta -.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -strictplus > test_msas\strictplus\example.049.AA.bctoNOG.ENOG4109AY5.fasta -.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -automated1 > test_msas\automated1\example.049.AA.bctoNOG.ENOG4109AY5.fasta -.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -nogaps > test_msas\nogaps\example.049.AA.bctoNOG.ENOG4109AY5.fasta -.\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -noallgaps > test_msas\noallgaps\example.049.AA.bctoNOG.ENOG4109AY5.fasta -.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -gappyout > test_msas\gappyout\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strict > test_msas\strict\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strictplus > test_msas\strictplus\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -automated1 > test_msas\automated1\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -nogaps > test_msas\nogaps\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -.\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -noallgaps > test_msas\noallgaps\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -gappyout > test_msas\gappyout\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strict > test_msas\strict\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strictplus > test_msas\strictplus\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -automated1 > test_msas\automated1\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -nogaps > test_msas\nogaps\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -.\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -noallgaps > test_msas\noallgaps\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -gappyout > test_msas\gappyout\example.052.AA.bctoNOG.ENOG4109CTU.fasta -.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -strict > test_msas\strict\example.052.AA.bctoNOG.ENOG4109CTU.fasta -.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -strictplus > test_msas\strictplus\example.052.AA.bctoNOG.ENOG4109CTU.fasta -.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -automated1 > test_msas\automated1\example.052.AA.bctoNOG.ENOG4109CTU.fasta -.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -nogaps > test_msas\nogaps\example.052.AA.bctoNOG.ENOG4109CTU.fasta -.\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -noallgaps > test_msas\noallgaps\example.052.AA.bctoNOG.ENOG4109CTU.fasta -.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -gappyout > test_msas\gappyout\example.053.AA.bctoNOG.ENOG4109CVC.fasta -.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -strict > test_msas\strict\example.053.AA.bctoNOG.ENOG4109CVC.fasta -.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -strictplus > test_msas\strictplus\example.053.AA.bctoNOG.ENOG4109CVC.fasta -.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -automated1 > test_msas\automated1\example.053.AA.bctoNOG.ENOG4109CVC.fasta -.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -nogaps > test_msas\nogaps\example.053.AA.bctoNOG.ENOG4109CVC.fasta -.\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -noallgaps > test_msas\noallgaps\example.053.AA.bctoNOG.ENOG4109CVC.fasta -.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -gappyout > test_msas\gappyout\example.054.AA.bctoNOG.ENOG4109FIT.fasta -.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -strict > test_msas\strict\example.054.AA.bctoNOG.ENOG4109FIT.fasta -.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -strictplus > test_msas\strictplus\example.054.AA.bctoNOG.ENOG4109FIT.fasta -.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -automated1 > test_msas\automated1\example.054.AA.bctoNOG.ENOG4109FIT.fasta -.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -nogaps > test_msas\nogaps\example.054.AA.bctoNOG.ENOG4109FIT.fasta -.\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -noallgaps > test_msas\noallgaps\example.054.AA.bctoNOG.ENOG4109FIT.fasta -.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -gappyout > test_msas\gappyout\example.055.AA.bctoNOG.ENOG4109GY9.fasta -.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -strict > test_msas\strict\example.055.AA.bctoNOG.ENOG4109GY9.fasta -.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -strictplus > test_msas\strictplus\example.055.AA.bctoNOG.ENOG4109GY9.fasta -.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -automated1 > test_msas\automated1\example.055.AA.bctoNOG.ENOG4109GY9.fasta -.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -nogaps > test_msas\nogaps\example.055.AA.bctoNOG.ENOG4109GY9.fasta -.\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -noallgaps > test_msas\noallgaps\example.055.AA.bctoNOG.ENOG4109GY9.fasta -.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -gappyout > test_msas\gappyout\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strict > test_msas\strict\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strictplus > test_msas\strictplus\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -automated1 > test_msas\automated1\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -nogaps > test_msas\nogaps\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -.\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -noallgaps > test_msas\noallgaps\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -gappyout > test_msas\gappyout\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strict > test_msas\strict\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strictplus > test_msas\strictplus\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -automated1 > test_msas\automated1\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -nogaps > test_msas\nogaps\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -.\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -noallgaps > test_msas\noallgaps\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -gappyout > test_msas\gappyout\example.058.AA.strNOG.ENOG411BBR6.fasta -.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -strict > test_msas\strict\example.058.AA.strNOG.ENOG411BBR6.fasta -.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -strictplus > test_msas\strictplus\example.058.AA.strNOG.ENOG411BBR6.fasta -.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -automated1 > test_msas\automated1\example.058.AA.strNOG.ENOG411BBR6.fasta -.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -nogaps > test_msas\nogaps\example.058.AA.strNOG.ENOG411BBR6.fasta -.\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -noallgaps > test_msas\noallgaps\example.058.AA.strNOG.ENOG411BBR6.fasta -.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -gappyout > test_msas\gappyout\example.059.AA.strNOG.ENOG411BBRR.fasta -.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -strict > test_msas\strict\example.059.AA.strNOG.ENOG411BBRR.fasta -.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -strictplus > test_msas\strictplus\example.059.AA.strNOG.ENOG411BBRR.fasta -.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -automated1 > test_msas\automated1\example.059.AA.strNOG.ENOG411BBRR.fasta -.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -nogaps > test_msas\nogaps\example.059.AA.strNOG.ENOG411BBRR.fasta -.\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -noallgaps > test_msas\noallgaps\example.059.AA.strNOG.ENOG411BBRR.fasta -.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -gappyout > test_msas\gappyout\example.060.AA.strNOG.ENOG411BBWK.fasta -.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -strict > test_msas\strict\example.060.AA.strNOG.ENOG411BBWK.fasta -.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -strictplus > test_msas\strictplus\example.060.AA.strNOG.ENOG411BBWK.fasta -.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -automated1 > test_msas\automated1\example.060.AA.strNOG.ENOG411BBWK.fasta -.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -nogaps > test_msas\nogaps\example.060.AA.strNOG.ENOG411BBWK.fasta -.\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -noallgaps > test_msas\noallgaps\example.060.AA.strNOG.ENOG411BBWK.fasta -.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -gappyout > test_msas\gappyout\example.061.AA.strNOG.ENOG411BCDZ.fasta -.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -strict > test_msas\strict\example.061.AA.strNOG.ENOG411BCDZ.fasta -.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -strictplus > test_msas\strictplus\example.061.AA.strNOG.ENOG411BCDZ.fasta -.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -automated1 > test_msas\automated1\example.061.AA.strNOG.ENOG411BCDZ.fasta -.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -nogaps > test_msas\nogaps\example.061.AA.strNOG.ENOG411BCDZ.fasta -.\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -noallgaps > test_msas\noallgaps\example.061.AA.strNOG.ENOG411BCDZ.fasta -.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -gappyout > test_msas\gappyout\example.062.AA.strNOG.ENOG411BCX3.fasta -.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -strict > test_msas\strict\example.062.AA.strNOG.ENOG411BCX3.fasta -.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -strictplus > test_msas\strictplus\example.062.AA.strNOG.ENOG411BCX3.fasta -.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -automated1 > test_msas\automated1\example.062.AA.strNOG.ENOG411BCX3.fasta -.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -nogaps > test_msas\nogaps\example.062.AA.strNOG.ENOG411BCX3.fasta -.\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -noallgaps > test_msas\noallgaps\example.062.AA.strNOG.ENOG411BCX3.fasta -.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -gappyout > test_msas\gappyout\example.063.AA.strNOG.ENOG411BDBU.fasta -.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -strict > test_msas\strict\example.063.AA.strNOG.ENOG411BDBU.fasta -.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -strictplus > test_msas\strictplus\example.063.AA.strNOG.ENOG411BDBU.fasta -.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -automated1 > test_msas\automated1\example.063.AA.strNOG.ENOG411BDBU.fasta -.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -nogaps > test_msas\nogaps\example.063.AA.strNOG.ENOG411BDBU.fasta -.\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -noallgaps > test_msas\noallgaps\example.063.AA.strNOG.ENOG411BDBU.fasta -.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -gappyout > test_msas\gappyout\example.064.AA.strNOG.ENOG411BDKC.fasta -.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -strict > test_msas\strict\example.064.AA.strNOG.ENOG411BDKC.fasta -.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -strictplus > test_msas\strictplus\example.064.AA.strNOG.ENOG411BDKC.fasta -.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -automated1 > test_msas\automated1\example.064.AA.strNOG.ENOG411BDKC.fasta -.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -nogaps > test_msas\nogaps\example.064.AA.strNOG.ENOG411BDKC.fasta -.\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -noallgaps > test_msas\noallgaps\example.064.AA.strNOG.ENOG411BDKC.fasta -.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -gappyout > test_msas\gappyout\example.065.AA.strNOG.ENOG411BDSZ.fasta -.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -strict > test_msas\strict\example.065.AA.strNOG.ENOG411BDSZ.fasta -.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -strictplus > test_msas\strictplus\example.065.AA.strNOG.ENOG411BDSZ.fasta -.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -automated1 > test_msas\automated1\example.065.AA.strNOG.ENOG411BDSZ.fasta -.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -nogaps > test_msas\nogaps\example.065.AA.strNOG.ENOG411BDSZ.fasta -.\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -noallgaps > test_msas\noallgaps\example.065.AA.strNOG.ENOG411BDSZ.fasta -.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -gappyout > test_msas\gappyout\example.066.AA.strNOG.ENOG411BDUE.fasta -.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -strict > test_msas\strict\example.066.AA.strNOG.ENOG411BDUE.fasta -.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -strictplus > test_msas\strictplus\example.066.AA.strNOG.ENOG411BDUE.fasta -.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -automated1 > test_msas\automated1\example.066.AA.strNOG.ENOG411BDUE.fasta -.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -nogaps > test_msas\nogaps\example.066.AA.strNOG.ENOG411BDUE.fasta -.\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -noallgaps > test_msas\noallgaps\example.066.AA.strNOG.ENOG411BDUE.fasta -.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -gappyout > test_msas\gappyout\example.067.AA.strNOG.ENOG411BDX3.fasta -.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -strict > test_msas\strict\example.067.AA.strNOG.ENOG411BDX3.fasta -.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -strictplus > test_msas\strictplus\example.067.AA.strNOG.ENOG411BDX3.fasta -.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -automated1 > test_msas\automated1\example.067.AA.strNOG.ENOG411BDX3.fasta -.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -nogaps > test_msas\nogaps\example.067.AA.strNOG.ENOG411BDX3.fasta -.\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -noallgaps > test_msas\noallgaps\example.067.AA.strNOG.ENOG411BDX3.fasta -.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -gappyout > test_msas\gappyout\example.068.AA.strNOG.ENOG411BE45.fasta -.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -strict > test_msas\strict\example.068.AA.strNOG.ENOG411BE45.fasta -.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -strictplus > test_msas\strictplus\example.068.AA.strNOG.ENOG411BE45.fasta -.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -automated1 > test_msas\automated1\example.068.AA.strNOG.ENOG411BE45.fasta -.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -nogaps > test_msas\nogaps\example.068.AA.strNOG.ENOG411BE45.fasta -.\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -noallgaps > test_msas\noallgaps\example.068.AA.strNOG.ENOG411BE45.fasta -.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -gappyout > test_msas\gappyout\example.069.AA.strNOG.ENOG411BE8B.fasta -.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -strict > test_msas\strict\example.069.AA.strNOG.ENOG411BE8B.fasta -.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -strictplus > test_msas\strictplus\example.069.AA.strNOG.ENOG411BE8B.fasta -.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -automated1 > test_msas\automated1\example.069.AA.strNOG.ENOG411BE8B.fasta -.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -nogaps > test_msas\nogaps\example.069.AA.strNOG.ENOG411BE8B.fasta -.\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -noallgaps > test_msas\noallgaps\example.069.AA.strNOG.ENOG411BE8B.fasta -.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -gappyout > test_msas\gappyout\example.070.AA.strNOG.ENOG411BEUV.fasta -.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -strict > test_msas\strict\example.070.AA.strNOG.ENOG411BEUV.fasta -.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -strictplus > test_msas\strictplus\example.070.AA.strNOG.ENOG411BEUV.fasta -.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -automated1 > test_msas\automated1\example.070.AA.strNOG.ENOG411BEUV.fasta -.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -nogaps > test_msas\nogaps\example.070.AA.strNOG.ENOG411BEUV.fasta -.\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -noallgaps > test_msas\noallgaps\example.070.AA.strNOG.ENOG411BEUV.fasta -.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -gappyout > test_msas\gappyout\example.071.AA.strNOG.ENOG411BEZ0.fasta -.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -strict > test_msas\strict\example.071.AA.strNOG.ENOG411BEZ0.fasta -.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -strictplus > test_msas\strictplus\example.071.AA.strNOG.ENOG411BEZ0.fasta -.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -automated1 > test_msas\automated1\example.071.AA.strNOG.ENOG411BEZ0.fasta -.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -nogaps > test_msas\nogaps\example.071.AA.strNOG.ENOG411BEZ0.fasta -.\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -noallgaps > test_msas\noallgaps\example.071.AA.strNOG.ENOG411BEZ0.fasta -.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -gappyout > test_msas\gappyout\example.072.AA.strNOG.ENOG411BF1S.fasta -.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -strict > test_msas\strict\example.072.AA.strNOG.ENOG411BF1S.fasta -.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -strictplus > test_msas\strictplus\example.072.AA.strNOG.ENOG411BF1S.fasta -.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -automated1 > test_msas\automated1\example.072.AA.strNOG.ENOG411BF1S.fasta -.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -nogaps > test_msas\nogaps\example.072.AA.strNOG.ENOG411BF1S.fasta -.\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -noallgaps > test_msas\noallgaps\example.072.AA.strNOG.ENOG411BF1S.fasta -.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -gappyout > test_msas\gappyout\example.073.AA.strNOG.ENOG411BFCW.fasta -.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -strict > test_msas\strict\example.073.AA.strNOG.ENOG411BFCW.fasta -.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -strictplus > test_msas\strictplus\example.073.AA.strNOG.ENOG411BFCW.fasta -.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -automated1 > test_msas\automated1\example.073.AA.strNOG.ENOG411BFCW.fasta -.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -nogaps > test_msas\nogaps\example.073.AA.strNOG.ENOG411BFCW.fasta -.\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -noallgaps > test_msas\noallgaps\example.073.AA.strNOG.ENOG411BFCW.fasta -.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -gappyout > test_msas\gappyout\example.074.AA.strNOG.ENOG411BFPF.fasta -.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -strict > test_msas\strict\example.074.AA.strNOG.ENOG411BFPF.fasta -.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -strictplus > test_msas\strictplus\example.074.AA.strNOG.ENOG411BFPF.fasta -.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -automated1 > test_msas\automated1\example.074.AA.strNOG.ENOG411BFPF.fasta -.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -nogaps > test_msas\nogaps\example.074.AA.strNOG.ENOG411BFPF.fasta -.\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -noallgaps > test_msas\noallgaps\example.074.AA.strNOG.ENOG411BFPF.fasta -.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -gappyout > test_msas\gappyout\example.075.AA.strNOG.ENOG411BFQS.fasta -.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -strict > test_msas\strict\example.075.AA.strNOG.ENOG411BFQS.fasta -.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -strictplus > test_msas\strictplus\example.075.AA.strNOG.ENOG411BFQS.fasta -.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -automated1 > test_msas\automated1\example.075.AA.strNOG.ENOG411BFQS.fasta -.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -nogaps > test_msas\nogaps\example.075.AA.strNOG.ENOG411BFQS.fasta -.\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -noallgaps > test_msas\noallgaps\example.075.AA.strNOG.ENOG411BFQS.fasta -.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -gappyout > test_msas\gappyout\example.076.AA.strNOG.ENOG411BH75.fasta -.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -strict > test_msas\strict\example.076.AA.strNOG.ENOG411BH75.fasta -.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -strictplus > test_msas\strictplus\example.076.AA.strNOG.ENOG411BH75.fasta -.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -automated1 > test_msas\automated1\example.076.AA.strNOG.ENOG411BH75.fasta -.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -nogaps > test_msas\nogaps\example.076.AA.strNOG.ENOG411BH75.fasta -.\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -noallgaps > test_msas\noallgaps\example.076.AA.strNOG.ENOG411BH75.fasta -.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -gappyout > test_msas\gappyout\example.077.AA.strNOG.ENOG411BH79.fasta -.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -strict > test_msas\strict\example.077.AA.strNOG.ENOG411BH79.fasta -.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -strictplus > test_msas\strictplus\example.077.AA.strNOG.ENOG411BH79.fasta -.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -automated1 > test_msas\automated1\example.077.AA.strNOG.ENOG411BH79.fasta -.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -nogaps > test_msas\nogaps\example.077.AA.strNOG.ENOG411BH79.fasta -.\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -noallgaps > test_msas\noallgaps\example.077.AA.strNOG.ENOG411BH79.fasta -.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -gappyout > test_msas\gappyout\example.078.AA.strNOG.ENOG411BH99.fasta -.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -strict > test_msas\strict\example.078.AA.strNOG.ENOG411BH99.fasta -.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -strictplus > test_msas\strictplus\example.078.AA.strNOG.ENOG411BH99.fasta -.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -automated1 > test_msas\automated1\example.078.AA.strNOG.ENOG411BH99.fasta -.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -nogaps > test_msas\nogaps\example.078.AA.strNOG.ENOG411BH99.fasta -.\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -noallgaps > test_msas\noallgaps\example.078.AA.strNOG.ENOG411BH99.fasta -.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -gappyout > test_msas\gappyout\example.079.AA.strNOG.ENOG411BJDC.fasta -.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -strict > test_msas\strict\example.079.AA.strNOG.ENOG411BJDC.fasta -.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -strictplus > test_msas\strictplus\example.079.AA.strNOG.ENOG411BJDC.fasta -.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -automated1 > test_msas\automated1\example.079.AA.strNOG.ENOG411BJDC.fasta -.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -nogaps > test_msas\nogaps\example.079.AA.strNOG.ENOG411BJDC.fasta -.\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -noallgaps > test_msas\noallgaps\example.079.AA.strNOG.ENOG411BJDC.fasta -.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -gappyout > test_msas\gappyout\example.080.AA.strNOG.ENOG411BJIF.fasta -.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -strict > test_msas\strict\example.080.AA.strNOG.ENOG411BJIF.fasta -.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -strictplus > test_msas\strictplus\example.080.AA.strNOG.ENOG411BJIF.fasta -.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -automated1 > test_msas\automated1\example.080.AA.strNOG.ENOG411BJIF.fasta -.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -nogaps > test_msas\nogaps\example.080.AA.strNOG.ENOG411BJIF.fasta -.\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -noallgaps > test_msas\noallgaps\example.080.AA.strNOG.ENOG411BJIF.fasta -.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -gappyout > test_msas\gappyout\example.081.AA.strNOG.ENOG411BK9X.fasta -.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -strict > test_msas\strict\example.081.AA.strNOG.ENOG411BK9X.fasta -.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -strictplus > test_msas\strictplus\example.081.AA.strNOG.ENOG411BK9X.fasta -.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -automated1 > test_msas\automated1\example.081.AA.strNOG.ENOG411BK9X.fasta -.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -nogaps > test_msas\nogaps\example.081.AA.strNOG.ENOG411BK9X.fasta -.\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -noallgaps > test_msas\noallgaps\example.081.AA.strNOG.ENOG411BK9X.fasta -.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -gappyout > test_msas\gappyout\example.082.AA.strNOG.ENOG411BKC5.fasta -.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -strict > test_msas\strict\example.082.AA.strNOG.ENOG411BKC5.fasta -.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -strictplus > test_msas\strictplus\example.082.AA.strNOG.ENOG411BKC5.fasta -.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -automated1 > test_msas\automated1\example.082.AA.strNOG.ENOG411BKC5.fasta -.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -nogaps > test_msas\nogaps\example.082.AA.strNOG.ENOG411BKC5.fasta -.\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -noallgaps > test_msas\noallgaps\example.082.AA.strNOG.ENOG411BKC5.fasta -.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -gappyout > test_msas\gappyout\example.083.AA.strNOG.ENOG411BMKC.fasta -.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -strict > test_msas\strict\example.083.AA.strNOG.ENOG411BMKC.fasta -.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -strictplus > test_msas\strictplus\example.083.AA.strNOG.ENOG411BMKC.fasta -.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -automated1 > test_msas\automated1\example.083.AA.strNOG.ENOG411BMKC.fasta -.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -nogaps > test_msas\nogaps\example.083.AA.strNOG.ENOG411BMKC.fasta -.\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -noallgaps > test_msas\noallgaps\example.083.AA.strNOG.ENOG411BMKC.fasta -.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -gappyout > test_msas\gappyout\example.084.AA.strNOG.ENOG411BNP9.fasta -.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -strict > test_msas\strict\example.084.AA.strNOG.ENOG411BNP9.fasta -.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -strictplus > test_msas\strictplus\example.084.AA.strNOG.ENOG411BNP9.fasta -.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -automated1 > test_msas\automated1\example.084.AA.strNOG.ENOG411BNP9.fasta -.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -nogaps > test_msas\nogaps\example.084.AA.strNOG.ENOG411BNP9.fasta -.\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -noallgaps > test_msas\noallgaps\example.084.AA.strNOG.ENOG411BNP9.fasta -.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -gappyout > test_msas\gappyout\example.085.AA.strNOG.ENOG411BQTJ.fasta -.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -strict > test_msas\strict\example.085.AA.strNOG.ENOG411BQTJ.fasta -.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -strictplus > test_msas\strictplus\example.085.AA.strNOG.ENOG411BQTJ.fasta -.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -automated1 > test_msas\automated1\example.085.AA.strNOG.ENOG411BQTJ.fasta -.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -nogaps > test_msas\nogaps\example.085.AA.strNOG.ENOG411BQTJ.fasta -.\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -noallgaps > test_msas\noallgaps\example.085.AA.strNOG.ENOG411BQTJ.fasta -.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -gappyout > test_msas\gappyout\example.086.AA.strNOG.ENOG411BR1D.fasta -.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -strict > test_msas\strict\example.086.AA.strNOG.ENOG411BR1D.fasta -.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -strictplus > test_msas\strictplus\example.086.AA.strNOG.ENOG411BR1D.fasta -.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -automated1 > test_msas\automated1\example.086.AA.strNOG.ENOG411BR1D.fasta -.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -nogaps > test_msas\nogaps\example.086.AA.strNOG.ENOG411BR1D.fasta -.\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -noallgaps > test_msas\noallgaps\example.086.AA.strNOG.ENOG411BR1D.fasta -.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -gappyout > test_msas\gappyout\example.087.AA.strNOG.ENOG411BRCH.fasta -.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -strict > test_msas\strict\example.087.AA.strNOG.ENOG411BRCH.fasta -.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -strictplus > test_msas\strictplus\example.087.AA.strNOG.ENOG411BRCH.fasta -.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -automated1 > test_msas\automated1\example.087.AA.strNOG.ENOG411BRCH.fasta -.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -nogaps > test_msas\nogaps\example.087.AA.strNOG.ENOG411BRCH.fasta -.\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -noallgaps > test_msas\noallgaps\example.087.AA.strNOG.ENOG411BRCH.fasta -.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -gappyout > test_msas\gappyout\example.088.AA.strNOG.ENOG411BSXF.fasta -.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -strict > test_msas\strict\example.088.AA.strNOG.ENOG411BSXF.fasta -.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -strictplus > test_msas\strictplus\example.088.AA.strNOG.ENOG411BSXF.fasta -.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -automated1 > test_msas\automated1\example.088.AA.strNOG.ENOG411BSXF.fasta -.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -nogaps > test_msas\nogaps\example.088.AA.strNOG.ENOG411BSXF.fasta -.\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -noallgaps > test_msas\noallgaps\example.088.AA.strNOG.ENOG411BSXF.fasta -.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -gappyout > test_msas\gappyout\example.089.AA.strNOG.ENOG411BV9B.fasta -.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -strict > test_msas\strict\example.089.AA.strNOG.ENOG411BV9B.fasta -.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -strictplus > test_msas\strictplus\example.089.AA.strNOG.ENOG411BV9B.fasta -.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -automated1 > test_msas\automated1\example.089.AA.strNOG.ENOG411BV9B.fasta -.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -nogaps > test_msas\nogaps\example.089.AA.strNOG.ENOG411BV9B.fasta -.\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -noallgaps > test_msas\noallgaps\example.089.AA.strNOG.ENOG411BV9B.fasta -.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -gappyout > test_msas\gappyout\example.090.AA.strNOG.ENOG411BVKR.fasta -.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -strict > test_msas\strict\example.090.AA.strNOG.ENOG411BVKR.fasta -.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -strictplus > test_msas\strictplus\example.090.AA.strNOG.ENOG411BVKR.fasta -.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -automated1 > test_msas\automated1\example.090.AA.strNOG.ENOG411BVKR.fasta -.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -nogaps > test_msas\nogaps\example.090.AA.strNOG.ENOG411BVKR.fasta -.\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -noallgaps > test_msas\noallgaps\example.090.AA.strNOG.ENOG411BVKR.fasta -.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -gappyout > test_msas\gappyout\example.091.AA.strNOG.ENOG411BWBU.fasta -.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -strict > test_msas\strict\example.091.AA.strNOG.ENOG411BWBU.fasta -.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -strictplus > test_msas\strictplus\example.091.AA.strNOG.ENOG411BWBU.fasta -.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -automated1 > test_msas\automated1\example.091.AA.strNOG.ENOG411BWBU.fasta -.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -nogaps > test_msas\nogaps\example.091.AA.strNOG.ENOG411BWBU.fasta -.\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -noallgaps > test_msas\noallgaps\example.091.AA.strNOG.ENOG411BWBU.fasta +.\source\trimal.exe -in dataset\example.004.AA.fasta -gappyout > test_msas\gappyout\example.004.AA.fasta +.\source\trimal.exe -in dataset\example.004.AA.fasta -strict > test_msas\strict\example.004.AA.fasta +.\source\trimal.exe -in dataset\example.004.AA.fasta -strictplus > test_msas\strictplus\example.004.AA.fasta +.\source\trimal.exe -in dataset\example.004.AA.fasta -automated1 > test_msas\automated1\example.004.AA.fasta +.\source\trimal.exe -in dataset\example.004.AA.fasta -nogaps > test_msas\nogaps\example.004.AA.fasta +.\source\trimal.exe -in dataset\example.004.AA.fasta -noallgaps > test_msas\noallgaps\example.004.AA.fasta +.\source\trimal.exe -in dataset\example.005.AA.fasta -gappyout > test_msas\gappyout\example.005.AA.fasta +.\source\trimal.exe -in dataset\example.005.AA.fasta -strict > test_msas\strict\example.005.AA.fasta +.\source\trimal.exe -in dataset\example.005.AA.fasta -strictplus > test_msas\strictplus\example.005.AA.fasta +.\source\trimal.exe -in dataset\example.005.AA.fasta -automated1 > test_msas\automated1\example.005.AA.fasta +.\source\trimal.exe -in dataset\example.005.AA.fasta -nogaps > test_msas\nogaps\example.005.AA.fasta +.\source\trimal.exe -in dataset\example.005.AA.fasta -noallgaps > test_msas\noallgaps\example.005.AA.fasta +.\source\trimal.exe -in dataset\example.007.AA.fasta -gappyout > test_msas\gappyout\example.007.AA.fasta +.\source\trimal.exe -in dataset\example.007.AA.fasta -strict > test_msas\strict\example.007.AA.fasta +.\source\trimal.exe -in dataset\example.007.AA.fasta -strictplus > test_msas\strictplus\example.007.AA.fasta +.\source\trimal.exe -in dataset\example.007.AA.fasta -automated1 > test_msas\automated1\example.007.AA.fasta +.\source\trimal.exe -in dataset\example.007.AA.fasta -nogaps > test_msas\nogaps\example.007.AA.fasta +.\source\trimal.exe -in dataset\example.007.AA.fasta -noallgaps > test_msas\noallgaps\example.007.AA.fasta +.\source\trimal.exe -in dataset\example.009.AA.fasta -gappyout > test_msas\gappyout\example.009.AA.fasta +.\source\trimal.exe -in dataset\example.009.AA.fasta -strict > test_msas\strict\example.009.AA.fasta +.\source\trimal.exe -in dataset\example.009.AA.fasta -strictplus > test_msas\strictplus\example.009.AA.fasta +.\source\trimal.exe -in dataset\example.009.AA.fasta -automated1 > test_msas\automated1\example.009.AA.fasta +.\source\trimal.exe -in dataset\example.009.AA.fasta -nogaps > test_msas\nogaps\example.009.AA.fasta +.\source\trimal.exe -in dataset\example.009.AA.fasta -noallgaps > test_msas\noallgaps\example.009.AA.fasta +.\source\trimal.exe -in dataset\example.010.AA.fasta -gappyout > test_msas\gappyout\example.010.AA.fasta +.\source\trimal.exe -in dataset\example.010.AA.fasta -strict > test_msas\strict\example.010.AA.fasta +.\source\trimal.exe -in dataset\example.010.AA.fasta -strictplus > test_msas\strictplus\example.010.AA.fasta +.\source\trimal.exe -in dataset\example.010.AA.fasta -automated1 > test_msas\automated1\example.010.AA.fasta +.\source\trimal.exe -in dataset\example.010.AA.fasta -nogaps > test_msas\nogaps\example.010.AA.fasta +.\source\trimal.exe -in dataset\example.010.AA.fasta -noallgaps > test_msas\noallgaps\example.010.AA.fasta +.\source\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -gappyout > test_msas\gappyout\example.011.AA.YKL197C.fasta +.\source\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -strict > test_msas\strict\example.011.AA.YKL197C.fasta +.\source\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -strictplus > test_msas\strictplus\example.011.AA.YKL197C.fasta +.\source\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -automated1 > test_msas\automated1\example.011.AA.YKL197C.fasta +.\source\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -nogaps > test_msas\nogaps\example.011.AA.YKL197C.fasta +.\source\trimal.exe -in dataset\example.011.AA.YKL197C.fasta -noallgaps > test_msas\noallgaps\example.011.AA.YKL197C.fasta +.\source\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -gappyout > test_msas\gappyout\example.014.AA.EggNOG.COG0591.fasta +.\source\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -strict > test_msas\strict\example.014.AA.EggNOG.COG0591.fasta +.\source\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -strictplus > test_msas\strictplus\example.014.AA.EggNOG.COG0591.fasta +.\source\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -automated1 > test_msas\automated1\example.014.AA.EggNOG.COG0591.fasta +.\source\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -nogaps > test_msas\nogaps\example.014.AA.EggNOG.COG0591.fasta +.\source\trimal.exe -in dataset\example.014.AA.EggNOG.COG0591.fasta -noallgaps > test_msas\noallgaps\example.014.AA.EggNOG.COG0591.fasta +.\source\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -gappyout > test_msas\gappyout\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\source\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -strict > test_msas\strict\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\source\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -strictplus > test_msas\strictplus\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\source\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -automated1 > test_msas\automated1\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\source\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -nogaps > test_msas\nogaps\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\source\trimal.exe -in dataset\example.015.AA.bctoNOG.ENOG41099F3.fasta -noallgaps > test_msas\noallgaps\example.015.AA.bctoNOG.ENOG41099F3.fasta +.\source\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -gappyout > test_msas\gappyout\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\source\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -strict > test_msas\strict\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\source\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -strictplus > test_msas\strictplus\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\source\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -automated1 > test_msas\automated1\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\source\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -nogaps > test_msas\nogaps\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\source\trimal.exe -in dataset\example.016.AA.bctoNOG.ENOG41099FB.fasta -noallgaps > test_msas\noallgaps\example.016.AA.bctoNOG.ENOG41099FB.fasta +.\source\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -gappyout > test_msas\gappyout\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\source\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -strict > test_msas\strict\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\source\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -strictplus > test_msas\strictplus\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\source\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -automated1 > test_msas\automated1\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\source\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -nogaps > test_msas\nogaps\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\source\trimal.exe -in dataset\example.017.AA.bctoNOG.ENOG41099FJ.fasta -noallgaps > test_msas\noallgaps\example.017.AA.bctoNOG.ENOG41099FJ.fasta +.\source\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -gappyout > test_msas\gappyout\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\source\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -strict > test_msas\strict\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\source\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -strictplus > test_msas\strictplus\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\source\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -automated1 > test_msas\automated1\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\source\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -nogaps > test_msas\nogaps\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\source\trimal.exe -in dataset\example.018.AA.bctoNOG.ENOG41099FV.fasta -noallgaps > test_msas\noallgaps\example.018.AA.bctoNOG.ENOG41099FV.fasta +.\source\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -gappyout > test_msas\gappyout\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\source\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -strict > test_msas\strict\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\source\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -strictplus > test_msas\strictplus\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\source\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -automated1 > test_msas\automated1\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\source\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -nogaps > test_msas\nogaps\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\source\trimal.exe -in dataset\example.019.AA.bctoNOG.ENOG41099HI.fasta -noallgaps > test_msas\noallgaps\example.019.AA.bctoNOG.ENOG41099HI.fasta +.\source\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -gappyout > test_msas\gappyout\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\source\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -strict > test_msas\strict\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\source\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -strictplus > test_msas\strictplus\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\source\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -automated1 > test_msas\automated1\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\source\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -nogaps > test_msas\nogaps\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\source\trimal.exe -in dataset\example.020.AA.bctoNOG.ENOG41099HN.fasta -noallgaps > test_msas\noallgaps\example.020.AA.bctoNOG.ENOG41099HN.fasta +.\source\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -gappyout > test_msas\gappyout\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\source\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -strict > test_msas\strict\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\source\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -strictplus > test_msas\strictplus\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\source\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -automated1 > test_msas\automated1\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\source\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -nogaps > test_msas\nogaps\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\source\trimal.exe -in dataset\example.021.AA.bctoNOG.ENOG41099I5.fasta -noallgaps > test_msas\noallgaps\example.021.AA.bctoNOG.ENOG41099I5.fasta +.\source\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -gappyout > test_msas\gappyout\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\source\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -strict > test_msas\strict\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\source\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -strictplus > test_msas\strictplus\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\source\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -automated1 > test_msas\automated1\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\source\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -nogaps > test_msas\nogaps\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\source\trimal.exe -in dataset\example.022.AA.bctoNOG.ENOG41099IZ.fasta -noallgaps > test_msas\noallgaps\example.022.AA.bctoNOG.ENOG41099IZ.fasta +.\source\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -gappyout > test_msas\gappyout\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\source\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -strict > test_msas\strict\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\source\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -strictplus > test_msas\strictplus\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\source\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -automated1 > test_msas\automated1\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\source\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -nogaps > test_msas\nogaps\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\source\trimal.exe -in dataset\example.023.AA.bctoNOG.ENOG41099K3.fasta -noallgaps > test_msas\noallgaps\example.023.AA.bctoNOG.ENOG41099K3.fasta +.\source\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -gappyout > test_msas\gappyout\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\source\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -strict > test_msas\strict\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\source\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -strictplus > test_msas\strictplus\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\source\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -automated1 > test_msas\automated1\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\source\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -nogaps > test_msas\nogaps\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\source\trimal.exe -in dataset\example.024.AA.bctoNOG.ENOG41099KM.fasta -noallgaps > test_msas\noallgaps\example.024.AA.bctoNOG.ENOG41099KM.fasta +.\source\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -gappyout > test_msas\gappyout\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\source\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -strict > test_msas\strict\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\source\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -strictplus > test_msas\strictplus\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\source\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -automated1 > test_msas\automated1\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\source\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -nogaps > test_msas\nogaps\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\source\trimal.exe -in dataset\example.025.AA.bctoNOG.ENOG41099KP.fasta -noallgaps > test_msas\noallgaps\example.025.AA.bctoNOG.ENOG41099KP.fasta +.\source\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -gappyout > test_msas\gappyout\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\source\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -strict > test_msas\strict\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\source\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -strictplus > test_msas\strictplus\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\source\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -automated1 > test_msas\automated1\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\source\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -nogaps > test_msas\nogaps\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\source\trimal.exe -in dataset\example.026.AA.bctoNOG.ENOG41099MV.fasta -noallgaps > test_msas\noallgaps\example.026.AA.bctoNOG.ENOG41099MV.fasta +.\source\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -gappyout > test_msas\gappyout\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\source\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -strict > test_msas\strict\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\source\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -strictplus > test_msas\strictplus\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\source\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -automated1 > test_msas\automated1\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\source\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -nogaps > test_msas\nogaps\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\source\trimal.exe -in dataset\example.027.AA.bctoNOG.ENOG41099NY.fasta -noallgaps > test_msas\noallgaps\example.027.AA.bctoNOG.ENOG41099NY.fasta +.\source\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -gappyout > test_msas\gappyout\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\source\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -strict > test_msas\strict\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\source\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -strictplus > test_msas\strictplus\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\source\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -automated1 > test_msas\automated1\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\source\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -nogaps > test_msas\nogaps\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\source\trimal.exe -in dataset\example.028.AA.bctoNOG.ENOG41099PA.fasta -noallgaps > test_msas\noallgaps\example.028.AA.bctoNOG.ENOG41099PA.fasta +.\source\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -gappyout > test_msas\gappyout\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\source\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -strict > test_msas\strict\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\source\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -strictplus > test_msas\strictplus\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\source\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -automated1 > test_msas\automated1\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\source\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -nogaps > test_msas\nogaps\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\source\trimal.exe -in dataset\example.029.AA.bctoNOG.ENOG41099Q3.fasta -noallgaps > test_msas\noallgaps\example.029.AA.bctoNOG.ENOG41099Q3.fasta +.\source\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -gappyout > test_msas\gappyout\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\source\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -strict > test_msas\strict\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\source\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -strictplus > test_msas\strictplus\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\source\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -automated1 > test_msas\automated1\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\source\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -nogaps > test_msas\nogaps\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\source\trimal.exe -in dataset\example.030.AA.bctoNOG.ENOG41099RG.fasta -noallgaps > test_msas\noallgaps\example.030.AA.bctoNOG.ENOG41099RG.fasta +.\source\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -gappyout > test_msas\gappyout\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\source\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -strict > test_msas\strict\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\source\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -strictplus > test_msas\strictplus\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\source\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -automated1 > test_msas\automated1\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\source\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -nogaps > test_msas\nogaps\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\source\trimal.exe -in dataset\example.031.AA.bctoNOG.ENOG41099UK.fasta -noallgaps > test_msas\noallgaps\example.031.AA.bctoNOG.ENOG41099UK.fasta +.\source\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -gappyout > test_msas\gappyout\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\source\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -strict > test_msas\strict\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\source\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -strictplus > test_msas\strictplus\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\source\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -automated1 > test_msas\automated1\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\source\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -nogaps > test_msas\nogaps\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\source\trimal.exe -in dataset\example.032.AA.bctoNOG.ENOG41099UW.fasta -noallgaps > test_msas\noallgaps\example.032.AA.bctoNOG.ENOG41099UW.fasta +.\source\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -gappyout > test_msas\gappyout\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\source\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -strict > test_msas\strict\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\source\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -strictplus > test_msas\strictplus\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\source\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -automated1 > test_msas\automated1\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\source\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -nogaps > test_msas\nogaps\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\source\trimal.exe -in dataset\example.033.AA.bctoNOG.ENOG41099VK.fasta -noallgaps > test_msas\noallgaps\example.033.AA.bctoNOG.ENOG41099VK.fasta +.\source\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -gappyout > test_msas\gappyout\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\source\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -strict > test_msas\strict\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\source\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -strictplus > test_msas\strictplus\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\source\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -automated1 > test_msas\automated1\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\source\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -nogaps > test_msas\nogaps\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\source\trimal.exe -in dataset\example.034.AA.bctoNOG.ENOG41099WA.fasta -noallgaps > test_msas\noallgaps\example.034.AA.bctoNOG.ENOG41099WA.fasta +.\source\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -gappyout > test_msas\gappyout\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\source\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -strict > test_msas\strict\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\source\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -strictplus > test_msas\strictplus\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\source\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -automated1 > test_msas\automated1\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\source\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -nogaps > test_msas\nogaps\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\source\trimal.exe -in dataset\example.035.AA.bctoNOG.ENOG41099WF.fasta -noallgaps > test_msas\noallgaps\example.035.AA.bctoNOG.ENOG41099WF.fasta +.\source\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -gappyout > test_msas\gappyout\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\source\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -strict > test_msas\strict\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\source\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -strictplus > test_msas\strictplus\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\source\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -automated1 > test_msas\automated1\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\source\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -nogaps > test_msas\nogaps\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\source\trimal.exe -in dataset\example.036.AA.bctoNOG.ENOG41099XJ.fasta -noallgaps > test_msas\noallgaps\example.036.AA.bctoNOG.ENOG41099XJ.fasta +.\source\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -gappyout > test_msas\gappyout\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\source\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -strict > test_msas\strict\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\source\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -strictplus > test_msas\strictplus\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\source\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -automated1 > test_msas\automated1\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\source\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -nogaps > test_msas\nogaps\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\source\trimal.exe -in dataset\example.037.AA.bctoNOG.ENOG41099XP.fasta -noallgaps > test_msas\noallgaps\example.037.AA.bctoNOG.ENOG41099XP.fasta +.\source\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -gappyout > test_msas\gappyout\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\source\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -strict > test_msas\strict\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\source\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -strictplus > test_msas\strictplus\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\source\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -automated1 > test_msas\automated1\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\source\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -nogaps > test_msas\nogaps\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\source\trimal.exe -in dataset\example.038.AA.bctoNOG.ENOG41099Y4.fasta -noallgaps > test_msas\noallgaps\example.038.AA.bctoNOG.ENOG41099Y4.fasta +.\source\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -gappyout > test_msas\gappyout\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\source\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -strict > test_msas\strict\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\source\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -strictplus > test_msas\strictplus\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\source\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -automated1 > test_msas\automated1\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\source\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -nogaps > test_msas\nogaps\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\source\trimal.exe -in dataset\example.039.AA.bctoNOG.ENOG41099YD.fasta -noallgaps > test_msas\noallgaps\example.039.AA.bctoNOG.ENOG41099YD.fasta +.\source\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -gappyout > test_msas\gappyout\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\source\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -strict > test_msas\strict\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\source\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -strictplus > test_msas\strictplus\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\source\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -automated1 > test_msas\automated1\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\source\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -nogaps > test_msas\nogaps\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\source\trimal.exe -in dataset\example.040.AA.bctoNOG.ENOG4109A32.fasta -noallgaps > test_msas\noallgaps\example.040.AA.bctoNOG.ENOG4109A32.fasta +.\source\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -gappyout > test_msas\gappyout\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\source\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -strict > test_msas\strict\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\source\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -strictplus > test_msas\strictplus\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\source\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -automated1 > test_msas\automated1\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\source\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -nogaps > test_msas\nogaps\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\source\trimal.exe -in dataset\example.041.AA.bctoNOG.ENOG4109A5T.fasta -noallgaps > test_msas\noallgaps\example.041.AA.bctoNOG.ENOG4109A5T.fasta +.\source\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -gappyout > test_msas\gappyout\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\source\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -strict > test_msas\strict\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\source\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -strictplus > test_msas\strictplus\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\source\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -automated1 > test_msas\automated1\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\source\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -nogaps > test_msas\nogaps\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\source\trimal.exe -in dataset\example.042.AA.bctoNOG.ENOG4109A9M.fasta -noallgaps > test_msas\noallgaps\example.042.AA.bctoNOG.ENOG4109A9M.fasta +.\source\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -gappyout > test_msas\gappyout\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\source\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -strict > test_msas\strict\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\source\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -strictplus > test_msas\strictplus\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\source\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -automated1 > test_msas\automated1\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\source\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -nogaps > test_msas\nogaps\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\source\trimal.exe -in dataset\example.043.AA.bctoNOG.ENOG4109ADN.fasta -noallgaps > test_msas\noallgaps\example.043.AA.bctoNOG.ENOG4109ADN.fasta +.\source\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -gappyout > test_msas\gappyout\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\source\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -strict > test_msas\strict\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\source\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -strictplus > test_msas\strictplus\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\source\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -automated1 > test_msas\automated1\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\source\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -nogaps > test_msas\nogaps\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\source\trimal.exe -in dataset\example.044.AA.bctoNOG.ENOG4109AED.fasta -noallgaps > test_msas\noallgaps\example.044.AA.bctoNOG.ENOG4109AED.fasta +.\source\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -gappyout > test_msas\gappyout\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\source\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -strict > test_msas\strict\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\source\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -strictplus > test_msas\strictplus\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\source\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -automated1 > test_msas\automated1\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\source\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -nogaps > test_msas\nogaps\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\source\trimal.exe -in dataset\example.045.AA.bctoNOG.ENOG4109AGT.fasta -noallgaps > test_msas\noallgaps\example.045.AA.bctoNOG.ENOG4109AGT.fasta +.\source\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -gappyout > test_msas\gappyout\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\source\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -strict > test_msas\strict\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\source\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -strictplus > test_msas\strictplus\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\source\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -automated1 > test_msas\automated1\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\source\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -nogaps > test_msas\nogaps\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\source\trimal.exe -in dataset\example.046.AA.bctoNOG.ENOG4109AGW.fasta -noallgaps > test_msas\noallgaps\example.046.AA.bctoNOG.ENOG4109AGW.fasta +.\source\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -gappyout > test_msas\gappyout\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\source\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -strict > test_msas\strict\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\source\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -strictplus > test_msas\strictplus\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\source\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -automated1 > test_msas\automated1\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\source\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -nogaps > test_msas\nogaps\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\source\trimal.exe -in dataset\example.047.AA.bctoNOG.ENOG4109AIC.fasta -noallgaps > test_msas\noallgaps\example.047.AA.bctoNOG.ENOG4109AIC.fasta +.\source\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -gappyout > test_msas\gappyout\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\source\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strict > test_msas\strict\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\source\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strictplus > test_msas\strictplus\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\source\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -automated1 > test_msas\automated1\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\source\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -nogaps > test_msas\nogaps\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\source\trimal.exe -in dataset\example.048.AA.bctoNOG.ENOG4109AJ3.fasta -noallgaps > test_msas\noallgaps\example.048.AA.bctoNOG.ENOG4109AJ3.fasta +.\source\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -gappyout > test_msas\gappyout\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\source\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -strict > test_msas\strict\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\source\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -strictplus > test_msas\strictplus\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\source\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -automated1 > test_msas\automated1\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\source\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -nogaps > test_msas\nogaps\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\source\trimal.exe -in dataset\example.049.AA.bctoNOG.ENOG4109AY5.fasta -noallgaps > test_msas\noallgaps\example.049.AA.bctoNOG.ENOG4109AY5.fasta +.\source\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -gappyout > test_msas\gappyout\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\source\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strict > test_msas\strict\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\source\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strictplus > test_msas\strictplus\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\source\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -automated1 > test_msas\automated1\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\source\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -nogaps > test_msas\nogaps\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\source\trimal.exe -in dataset\example.050.AA.bctoNOG.ENOG4109B8Z.fasta -noallgaps > test_msas\noallgaps\example.050.AA.bctoNOG.ENOG4109B8Z.fasta +.\source\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -gappyout > test_msas\gappyout\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\source\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strict > test_msas\strict\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\source\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strictplus > test_msas\strictplus\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\source\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -automated1 > test_msas\automated1\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\source\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -nogaps > test_msas\nogaps\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\source\trimal.exe -in dataset\example.051.AA.bctoNOG.ENOG4109BCJ.fasta -noallgaps > test_msas\noallgaps\example.051.AA.bctoNOG.ENOG4109BCJ.fasta +.\source\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -gappyout > test_msas\gappyout\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\source\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -strict > test_msas\strict\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\source\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -strictplus > test_msas\strictplus\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\source\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -automated1 > test_msas\automated1\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\source\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -nogaps > test_msas\nogaps\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\source\trimal.exe -in dataset\example.052.AA.bctoNOG.ENOG4109CTU.fasta -noallgaps > test_msas\noallgaps\example.052.AA.bctoNOG.ENOG4109CTU.fasta +.\source\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -gappyout > test_msas\gappyout\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\source\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -strict > test_msas\strict\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\source\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -strictplus > test_msas\strictplus\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\source\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -automated1 > test_msas\automated1\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\source\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -nogaps > test_msas\nogaps\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\source\trimal.exe -in dataset\example.053.AA.bctoNOG.ENOG4109CVC.fasta -noallgaps > test_msas\noallgaps\example.053.AA.bctoNOG.ENOG4109CVC.fasta +.\source\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -gappyout > test_msas\gappyout\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\source\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -strict > test_msas\strict\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\source\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -strictplus > test_msas\strictplus\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\source\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -automated1 > test_msas\automated1\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\source\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -nogaps > test_msas\nogaps\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\source\trimal.exe -in dataset\example.054.AA.bctoNOG.ENOG4109FIT.fasta -noallgaps > test_msas\noallgaps\example.054.AA.bctoNOG.ENOG4109FIT.fasta +.\source\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -gappyout > test_msas\gappyout\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\source\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -strict > test_msas\strict\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\source\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -strictplus > test_msas\strictplus\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\source\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -automated1 > test_msas\automated1\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\source\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -nogaps > test_msas\nogaps\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\source\trimal.exe -in dataset\example.055.AA.bctoNOG.ENOG4109GY9.fasta -noallgaps > test_msas\noallgaps\example.055.AA.bctoNOG.ENOG4109GY9.fasta +.\source\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -gappyout > test_msas\gappyout\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\source\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strict > test_msas\strict\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\source\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strictplus > test_msas\strictplus\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\source\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -automated1 > test_msas\automated1\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\source\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -nogaps > test_msas\nogaps\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\source\trimal.exe -in dataset\example.056.AA.bctoNOG.ENOG4109IPJ.fasta -noallgaps > test_msas\noallgaps\example.056.AA.bctoNOG.ENOG4109IPJ.fasta +.\source\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -gappyout > test_msas\gappyout\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\source\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strict > test_msas\strict\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\source\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strictplus > test_msas\strictplus\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\source\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -automated1 > test_msas\automated1\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\source\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -nogaps > test_msas\nogaps\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\source\trimal.exe -in dataset\example.057.AA.bctoNOG.ENOG4109SZ2.fasta -noallgaps > test_msas\noallgaps\example.057.AA.bctoNOG.ENOG4109SZ2.fasta +.\source\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -gappyout > test_msas\gappyout\example.058.AA.strNOG.ENOG411BBR6.fasta +.\source\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -strict > test_msas\strict\example.058.AA.strNOG.ENOG411BBR6.fasta +.\source\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -strictplus > test_msas\strictplus\example.058.AA.strNOG.ENOG411BBR6.fasta +.\source\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -automated1 > test_msas\automated1\example.058.AA.strNOG.ENOG411BBR6.fasta +.\source\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -nogaps > test_msas\nogaps\example.058.AA.strNOG.ENOG411BBR6.fasta +.\source\trimal.exe -in dataset\example.058.AA.strNOG.ENOG411BBR6.fasta -noallgaps > test_msas\noallgaps\example.058.AA.strNOG.ENOG411BBR6.fasta +.\source\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -gappyout > test_msas\gappyout\example.059.AA.strNOG.ENOG411BBRR.fasta +.\source\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -strict > test_msas\strict\example.059.AA.strNOG.ENOG411BBRR.fasta +.\source\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -strictplus > test_msas\strictplus\example.059.AA.strNOG.ENOG411BBRR.fasta +.\source\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -automated1 > test_msas\automated1\example.059.AA.strNOG.ENOG411BBRR.fasta +.\source\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -nogaps > test_msas\nogaps\example.059.AA.strNOG.ENOG411BBRR.fasta +.\source\trimal.exe -in dataset\example.059.AA.strNOG.ENOG411BBRR.fasta -noallgaps > test_msas\noallgaps\example.059.AA.strNOG.ENOG411BBRR.fasta +.\source\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -gappyout > test_msas\gappyout\example.060.AA.strNOG.ENOG411BBWK.fasta +.\source\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -strict > test_msas\strict\example.060.AA.strNOG.ENOG411BBWK.fasta +.\source\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -strictplus > test_msas\strictplus\example.060.AA.strNOG.ENOG411BBWK.fasta +.\source\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -automated1 > test_msas\automated1\example.060.AA.strNOG.ENOG411BBWK.fasta +.\source\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -nogaps > test_msas\nogaps\example.060.AA.strNOG.ENOG411BBWK.fasta +.\source\trimal.exe -in dataset\example.060.AA.strNOG.ENOG411BBWK.fasta -noallgaps > test_msas\noallgaps\example.060.AA.strNOG.ENOG411BBWK.fasta +.\source\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -gappyout > test_msas\gappyout\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\source\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -strict > test_msas\strict\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\source\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -strictplus > test_msas\strictplus\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\source\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -automated1 > test_msas\automated1\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\source\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -nogaps > test_msas\nogaps\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\source\trimal.exe -in dataset\example.061.AA.strNOG.ENOG411BCDZ.fasta -noallgaps > test_msas\noallgaps\example.061.AA.strNOG.ENOG411BCDZ.fasta +.\source\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -gappyout > test_msas\gappyout\example.062.AA.strNOG.ENOG411BCX3.fasta +.\source\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -strict > test_msas\strict\example.062.AA.strNOG.ENOG411BCX3.fasta +.\source\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -strictplus > test_msas\strictplus\example.062.AA.strNOG.ENOG411BCX3.fasta +.\source\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -automated1 > test_msas\automated1\example.062.AA.strNOG.ENOG411BCX3.fasta +.\source\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -nogaps > test_msas\nogaps\example.062.AA.strNOG.ENOG411BCX3.fasta +.\source\trimal.exe -in dataset\example.062.AA.strNOG.ENOG411BCX3.fasta -noallgaps > test_msas\noallgaps\example.062.AA.strNOG.ENOG411BCX3.fasta +.\source\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -gappyout > test_msas\gappyout\example.063.AA.strNOG.ENOG411BDBU.fasta +.\source\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -strict > test_msas\strict\example.063.AA.strNOG.ENOG411BDBU.fasta +.\source\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -strictplus > test_msas\strictplus\example.063.AA.strNOG.ENOG411BDBU.fasta +.\source\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -automated1 > test_msas\automated1\example.063.AA.strNOG.ENOG411BDBU.fasta +.\source\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -nogaps > test_msas\nogaps\example.063.AA.strNOG.ENOG411BDBU.fasta +.\source\trimal.exe -in dataset\example.063.AA.strNOG.ENOG411BDBU.fasta -noallgaps > test_msas\noallgaps\example.063.AA.strNOG.ENOG411BDBU.fasta +.\source\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -gappyout > test_msas\gappyout\example.064.AA.strNOG.ENOG411BDKC.fasta +.\source\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -strict > test_msas\strict\example.064.AA.strNOG.ENOG411BDKC.fasta +.\source\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -strictplus > test_msas\strictplus\example.064.AA.strNOG.ENOG411BDKC.fasta +.\source\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -automated1 > test_msas\automated1\example.064.AA.strNOG.ENOG411BDKC.fasta +.\source\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -nogaps > test_msas\nogaps\example.064.AA.strNOG.ENOG411BDKC.fasta +.\source\trimal.exe -in dataset\example.064.AA.strNOG.ENOG411BDKC.fasta -noallgaps > test_msas\noallgaps\example.064.AA.strNOG.ENOG411BDKC.fasta +.\source\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -gappyout > test_msas\gappyout\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\source\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -strict > test_msas\strict\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\source\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -strictplus > test_msas\strictplus\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\source\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -automated1 > test_msas\automated1\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\source\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -nogaps > test_msas\nogaps\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\source\trimal.exe -in dataset\example.065.AA.strNOG.ENOG411BDSZ.fasta -noallgaps > test_msas\noallgaps\example.065.AA.strNOG.ENOG411BDSZ.fasta +.\source\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -gappyout > test_msas\gappyout\example.066.AA.strNOG.ENOG411BDUE.fasta +.\source\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -strict > test_msas\strict\example.066.AA.strNOG.ENOG411BDUE.fasta +.\source\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -strictplus > test_msas\strictplus\example.066.AA.strNOG.ENOG411BDUE.fasta +.\source\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -automated1 > test_msas\automated1\example.066.AA.strNOG.ENOG411BDUE.fasta +.\source\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -nogaps > test_msas\nogaps\example.066.AA.strNOG.ENOG411BDUE.fasta +.\source\trimal.exe -in dataset\example.066.AA.strNOG.ENOG411BDUE.fasta -noallgaps > test_msas\noallgaps\example.066.AA.strNOG.ENOG411BDUE.fasta +.\source\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -gappyout > test_msas\gappyout\example.067.AA.strNOG.ENOG411BDX3.fasta +.\source\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -strict > test_msas\strict\example.067.AA.strNOG.ENOG411BDX3.fasta +.\source\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -strictplus > test_msas\strictplus\example.067.AA.strNOG.ENOG411BDX3.fasta +.\source\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -automated1 > test_msas\automated1\example.067.AA.strNOG.ENOG411BDX3.fasta +.\source\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -nogaps > test_msas\nogaps\example.067.AA.strNOG.ENOG411BDX3.fasta +.\source\trimal.exe -in dataset\example.067.AA.strNOG.ENOG411BDX3.fasta -noallgaps > test_msas\noallgaps\example.067.AA.strNOG.ENOG411BDX3.fasta +.\source\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -gappyout > test_msas\gappyout\example.068.AA.strNOG.ENOG411BE45.fasta +.\source\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -strict > test_msas\strict\example.068.AA.strNOG.ENOG411BE45.fasta +.\source\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -strictplus > test_msas\strictplus\example.068.AA.strNOG.ENOG411BE45.fasta +.\source\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -automated1 > test_msas\automated1\example.068.AA.strNOG.ENOG411BE45.fasta +.\source\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -nogaps > test_msas\nogaps\example.068.AA.strNOG.ENOG411BE45.fasta +.\source\trimal.exe -in dataset\example.068.AA.strNOG.ENOG411BE45.fasta -noallgaps > test_msas\noallgaps\example.068.AA.strNOG.ENOG411BE45.fasta +.\source\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -gappyout > test_msas\gappyout\example.069.AA.strNOG.ENOG411BE8B.fasta +.\source\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -strict > test_msas\strict\example.069.AA.strNOG.ENOG411BE8B.fasta +.\source\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -strictplus > test_msas\strictplus\example.069.AA.strNOG.ENOG411BE8B.fasta +.\source\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -automated1 > test_msas\automated1\example.069.AA.strNOG.ENOG411BE8B.fasta +.\source\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -nogaps > test_msas\nogaps\example.069.AA.strNOG.ENOG411BE8B.fasta +.\source\trimal.exe -in dataset\example.069.AA.strNOG.ENOG411BE8B.fasta -noallgaps > test_msas\noallgaps\example.069.AA.strNOG.ENOG411BE8B.fasta +.\source\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -gappyout > test_msas\gappyout\example.070.AA.strNOG.ENOG411BEUV.fasta +.\source\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -strict > test_msas\strict\example.070.AA.strNOG.ENOG411BEUV.fasta +.\source\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -strictplus > test_msas\strictplus\example.070.AA.strNOG.ENOG411BEUV.fasta +.\source\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -automated1 > test_msas\automated1\example.070.AA.strNOG.ENOG411BEUV.fasta +.\source\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -nogaps > test_msas\nogaps\example.070.AA.strNOG.ENOG411BEUV.fasta +.\source\trimal.exe -in dataset\example.070.AA.strNOG.ENOG411BEUV.fasta -noallgaps > test_msas\noallgaps\example.070.AA.strNOG.ENOG411BEUV.fasta +.\source\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -gappyout > test_msas\gappyout\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\source\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -strict > test_msas\strict\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\source\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -strictplus > test_msas\strictplus\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\source\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -automated1 > test_msas\automated1\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\source\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -nogaps > test_msas\nogaps\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\source\trimal.exe -in dataset\example.071.AA.strNOG.ENOG411BEZ0.fasta -noallgaps > test_msas\noallgaps\example.071.AA.strNOG.ENOG411BEZ0.fasta +.\source\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -gappyout > test_msas\gappyout\example.072.AA.strNOG.ENOG411BF1S.fasta +.\source\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -strict > test_msas\strict\example.072.AA.strNOG.ENOG411BF1S.fasta +.\source\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -strictplus > test_msas\strictplus\example.072.AA.strNOG.ENOG411BF1S.fasta +.\source\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -automated1 > test_msas\automated1\example.072.AA.strNOG.ENOG411BF1S.fasta +.\source\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -nogaps > test_msas\nogaps\example.072.AA.strNOG.ENOG411BF1S.fasta +.\source\trimal.exe -in dataset\example.072.AA.strNOG.ENOG411BF1S.fasta -noallgaps > test_msas\noallgaps\example.072.AA.strNOG.ENOG411BF1S.fasta +.\source\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -gappyout > test_msas\gappyout\example.073.AA.strNOG.ENOG411BFCW.fasta +.\source\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -strict > test_msas\strict\example.073.AA.strNOG.ENOG411BFCW.fasta +.\source\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -strictplus > test_msas\strictplus\example.073.AA.strNOG.ENOG411BFCW.fasta +.\source\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -automated1 > test_msas\automated1\example.073.AA.strNOG.ENOG411BFCW.fasta +.\source\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -nogaps > test_msas\nogaps\example.073.AA.strNOG.ENOG411BFCW.fasta +.\source\trimal.exe -in dataset\example.073.AA.strNOG.ENOG411BFCW.fasta -noallgaps > test_msas\noallgaps\example.073.AA.strNOG.ENOG411BFCW.fasta +.\source\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -gappyout > test_msas\gappyout\example.074.AA.strNOG.ENOG411BFPF.fasta +.\source\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -strict > test_msas\strict\example.074.AA.strNOG.ENOG411BFPF.fasta +.\source\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -strictplus > test_msas\strictplus\example.074.AA.strNOG.ENOG411BFPF.fasta +.\source\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -automated1 > test_msas\automated1\example.074.AA.strNOG.ENOG411BFPF.fasta +.\source\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -nogaps > test_msas\nogaps\example.074.AA.strNOG.ENOG411BFPF.fasta +.\source\trimal.exe -in dataset\example.074.AA.strNOG.ENOG411BFPF.fasta -noallgaps > test_msas\noallgaps\example.074.AA.strNOG.ENOG411BFPF.fasta +.\source\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -gappyout > test_msas\gappyout\example.075.AA.strNOG.ENOG411BFQS.fasta +.\source\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -strict > test_msas\strict\example.075.AA.strNOG.ENOG411BFQS.fasta +.\source\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -strictplus > test_msas\strictplus\example.075.AA.strNOG.ENOG411BFQS.fasta +.\source\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -automated1 > test_msas\automated1\example.075.AA.strNOG.ENOG411BFQS.fasta +.\source\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -nogaps > test_msas\nogaps\example.075.AA.strNOG.ENOG411BFQS.fasta +.\source\trimal.exe -in dataset\example.075.AA.strNOG.ENOG411BFQS.fasta -noallgaps > test_msas\noallgaps\example.075.AA.strNOG.ENOG411BFQS.fasta +.\source\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -gappyout > test_msas\gappyout\example.076.AA.strNOG.ENOG411BH75.fasta +.\source\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -strict > test_msas\strict\example.076.AA.strNOG.ENOG411BH75.fasta +.\source\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -strictplus > test_msas\strictplus\example.076.AA.strNOG.ENOG411BH75.fasta +.\source\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -automated1 > test_msas\automated1\example.076.AA.strNOG.ENOG411BH75.fasta +.\source\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -nogaps > test_msas\nogaps\example.076.AA.strNOG.ENOG411BH75.fasta +.\source\trimal.exe -in dataset\example.076.AA.strNOG.ENOG411BH75.fasta -noallgaps > test_msas\noallgaps\example.076.AA.strNOG.ENOG411BH75.fasta +.\source\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -gappyout > test_msas\gappyout\example.077.AA.strNOG.ENOG411BH79.fasta +.\source\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -strict > test_msas\strict\example.077.AA.strNOG.ENOG411BH79.fasta +.\source\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -strictplus > test_msas\strictplus\example.077.AA.strNOG.ENOG411BH79.fasta +.\source\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -automated1 > test_msas\automated1\example.077.AA.strNOG.ENOG411BH79.fasta +.\source\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -nogaps > test_msas\nogaps\example.077.AA.strNOG.ENOG411BH79.fasta +.\source\trimal.exe -in dataset\example.077.AA.strNOG.ENOG411BH79.fasta -noallgaps > test_msas\noallgaps\example.077.AA.strNOG.ENOG411BH79.fasta +.\source\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -gappyout > test_msas\gappyout\example.078.AA.strNOG.ENOG411BH99.fasta +.\source\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -strict > test_msas\strict\example.078.AA.strNOG.ENOG411BH99.fasta +.\source\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -strictplus > test_msas\strictplus\example.078.AA.strNOG.ENOG411BH99.fasta +.\source\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -automated1 > test_msas\automated1\example.078.AA.strNOG.ENOG411BH99.fasta +.\source\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -nogaps > test_msas\nogaps\example.078.AA.strNOG.ENOG411BH99.fasta +.\source\trimal.exe -in dataset\example.078.AA.strNOG.ENOG411BH99.fasta -noallgaps > test_msas\noallgaps\example.078.AA.strNOG.ENOG411BH99.fasta +.\source\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -gappyout > test_msas\gappyout\example.079.AA.strNOG.ENOG411BJDC.fasta +.\source\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -strict > test_msas\strict\example.079.AA.strNOG.ENOG411BJDC.fasta +.\source\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -strictplus > test_msas\strictplus\example.079.AA.strNOG.ENOG411BJDC.fasta +.\source\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -automated1 > test_msas\automated1\example.079.AA.strNOG.ENOG411BJDC.fasta +.\source\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -nogaps > test_msas\nogaps\example.079.AA.strNOG.ENOG411BJDC.fasta +.\source\trimal.exe -in dataset\example.079.AA.strNOG.ENOG411BJDC.fasta -noallgaps > test_msas\noallgaps\example.079.AA.strNOG.ENOG411BJDC.fasta +.\source\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -gappyout > test_msas\gappyout\example.080.AA.strNOG.ENOG411BJIF.fasta +.\source\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -strict > test_msas\strict\example.080.AA.strNOG.ENOG411BJIF.fasta +.\source\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -strictplus > test_msas\strictplus\example.080.AA.strNOG.ENOG411BJIF.fasta +.\source\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -automated1 > test_msas\automated1\example.080.AA.strNOG.ENOG411BJIF.fasta +.\source\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -nogaps > test_msas\nogaps\example.080.AA.strNOG.ENOG411BJIF.fasta +.\source\trimal.exe -in dataset\example.080.AA.strNOG.ENOG411BJIF.fasta -noallgaps > test_msas\noallgaps\example.080.AA.strNOG.ENOG411BJIF.fasta +.\source\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -gappyout > test_msas\gappyout\example.081.AA.strNOG.ENOG411BK9X.fasta +.\source\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -strict > test_msas\strict\example.081.AA.strNOG.ENOG411BK9X.fasta +.\source\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -strictplus > test_msas\strictplus\example.081.AA.strNOG.ENOG411BK9X.fasta +.\source\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -automated1 > test_msas\automated1\example.081.AA.strNOG.ENOG411BK9X.fasta +.\source\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -nogaps > test_msas\nogaps\example.081.AA.strNOG.ENOG411BK9X.fasta +.\source\trimal.exe -in dataset\example.081.AA.strNOG.ENOG411BK9X.fasta -noallgaps > test_msas\noallgaps\example.081.AA.strNOG.ENOG411BK9X.fasta +.\source\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -gappyout > test_msas\gappyout\example.082.AA.strNOG.ENOG411BKC5.fasta +.\source\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -strict > test_msas\strict\example.082.AA.strNOG.ENOG411BKC5.fasta +.\source\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -strictplus > test_msas\strictplus\example.082.AA.strNOG.ENOG411BKC5.fasta +.\source\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -automated1 > test_msas\automated1\example.082.AA.strNOG.ENOG411BKC5.fasta +.\source\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -nogaps > test_msas\nogaps\example.082.AA.strNOG.ENOG411BKC5.fasta +.\source\trimal.exe -in dataset\example.082.AA.strNOG.ENOG411BKC5.fasta -noallgaps > test_msas\noallgaps\example.082.AA.strNOG.ENOG411BKC5.fasta +.\source\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -gappyout > test_msas\gappyout\example.083.AA.strNOG.ENOG411BMKC.fasta +.\source\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -strict > test_msas\strict\example.083.AA.strNOG.ENOG411BMKC.fasta +.\source\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -strictplus > test_msas\strictplus\example.083.AA.strNOG.ENOG411BMKC.fasta +.\source\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -automated1 > test_msas\automated1\example.083.AA.strNOG.ENOG411BMKC.fasta +.\source\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -nogaps > test_msas\nogaps\example.083.AA.strNOG.ENOG411BMKC.fasta +.\source\trimal.exe -in dataset\example.083.AA.strNOG.ENOG411BMKC.fasta -noallgaps > test_msas\noallgaps\example.083.AA.strNOG.ENOG411BMKC.fasta +.\source\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -gappyout > test_msas\gappyout\example.084.AA.strNOG.ENOG411BNP9.fasta +.\source\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -strict > test_msas\strict\example.084.AA.strNOG.ENOG411BNP9.fasta +.\source\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -strictplus > test_msas\strictplus\example.084.AA.strNOG.ENOG411BNP9.fasta +.\source\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -automated1 > test_msas\automated1\example.084.AA.strNOG.ENOG411BNP9.fasta +.\source\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -nogaps > test_msas\nogaps\example.084.AA.strNOG.ENOG411BNP9.fasta +.\source\trimal.exe -in dataset\example.084.AA.strNOG.ENOG411BNP9.fasta -noallgaps > test_msas\noallgaps\example.084.AA.strNOG.ENOG411BNP9.fasta +.\source\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -gappyout > test_msas\gappyout\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\source\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -strict > test_msas\strict\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\source\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -strictplus > test_msas\strictplus\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\source\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -automated1 > test_msas\automated1\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\source\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -nogaps > test_msas\nogaps\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\source\trimal.exe -in dataset\example.085.AA.strNOG.ENOG411BQTJ.fasta -noallgaps > test_msas\noallgaps\example.085.AA.strNOG.ENOG411BQTJ.fasta +.\source\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -gappyout > test_msas\gappyout\example.086.AA.strNOG.ENOG411BR1D.fasta +.\source\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -strict > test_msas\strict\example.086.AA.strNOG.ENOG411BR1D.fasta +.\source\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -strictplus > test_msas\strictplus\example.086.AA.strNOG.ENOG411BR1D.fasta +.\source\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -automated1 > test_msas\automated1\example.086.AA.strNOG.ENOG411BR1D.fasta +.\source\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -nogaps > test_msas\nogaps\example.086.AA.strNOG.ENOG411BR1D.fasta +.\source\trimal.exe -in dataset\example.086.AA.strNOG.ENOG411BR1D.fasta -noallgaps > test_msas\noallgaps\example.086.AA.strNOG.ENOG411BR1D.fasta +.\source\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -gappyout > test_msas\gappyout\example.087.AA.strNOG.ENOG411BRCH.fasta +.\source\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -strict > test_msas\strict\example.087.AA.strNOG.ENOG411BRCH.fasta +.\source\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -strictplus > test_msas\strictplus\example.087.AA.strNOG.ENOG411BRCH.fasta +.\source\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -automated1 > test_msas\automated1\example.087.AA.strNOG.ENOG411BRCH.fasta +.\source\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -nogaps > test_msas\nogaps\example.087.AA.strNOG.ENOG411BRCH.fasta +.\source\trimal.exe -in dataset\example.087.AA.strNOG.ENOG411BRCH.fasta -noallgaps > test_msas\noallgaps\example.087.AA.strNOG.ENOG411BRCH.fasta +.\source\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -gappyout > test_msas\gappyout\example.088.AA.strNOG.ENOG411BSXF.fasta +.\source\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -strict > test_msas\strict\example.088.AA.strNOG.ENOG411BSXF.fasta +.\source\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -strictplus > test_msas\strictplus\example.088.AA.strNOG.ENOG411BSXF.fasta +.\source\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -automated1 > test_msas\automated1\example.088.AA.strNOG.ENOG411BSXF.fasta +.\source\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -nogaps > test_msas\nogaps\example.088.AA.strNOG.ENOG411BSXF.fasta +.\source\trimal.exe -in dataset\example.088.AA.strNOG.ENOG411BSXF.fasta -noallgaps > test_msas\noallgaps\example.088.AA.strNOG.ENOG411BSXF.fasta +.\source\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -gappyout > test_msas\gappyout\example.089.AA.strNOG.ENOG411BV9B.fasta +.\source\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -strict > test_msas\strict\example.089.AA.strNOG.ENOG411BV9B.fasta +.\source\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -strictplus > test_msas\strictplus\example.089.AA.strNOG.ENOG411BV9B.fasta +.\source\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -automated1 > test_msas\automated1\example.089.AA.strNOG.ENOG411BV9B.fasta +.\source\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -nogaps > test_msas\nogaps\example.089.AA.strNOG.ENOG411BV9B.fasta +.\source\trimal.exe -in dataset\example.089.AA.strNOG.ENOG411BV9B.fasta -noallgaps > test_msas\noallgaps\example.089.AA.strNOG.ENOG411BV9B.fasta +.\source\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -gappyout > test_msas\gappyout\example.090.AA.strNOG.ENOG411BVKR.fasta +.\source\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -strict > test_msas\strict\example.090.AA.strNOG.ENOG411BVKR.fasta +.\source\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -strictplus > test_msas\strictplus\example.090.AA.strNOG.ENOG411BVKR.fasta +.\source\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -automated1 > test_msas\automated1\example.090.AA.strNOG.ENOG411BVKR.fasta +.\source\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -nogaps > test_msas\nogaps\example.090.AA.strNOG.ENOG411BVKR.fasta +.\source\trimal.exe -in dataset\example.090.AA.strNOG.ENOG411BVKR.fasta -noallgaps > test_msas\noallgaps\example.090.AA.strNOG.ENOG411BVKR.fasta +.\source\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -gappyout > test_msas\gappyout\example.091.AA.strNOG.ENOG411BWBU.fasta +.\source\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -strict > test_msas\strict\example.091.AA.strNOG.ENOG411BWBU.fasta +.\source\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -strictplus > test_msas\strictplus\example.091.AA.strNOG.ENOG411BWBU.fasta +.\source\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -automated1 > test_msas\automated1\example.091.AA.strNOG.ENOG411BWBU.fasta +.\source\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -nogaps > test_msas\nogaps\example.091.AA.strNOG.ENOG411BWBU.fasta +.\source\trimal.exe -in dataset\example.091.AA.strNOG.ENOG411BWBU.fasta -noallgaps > test_msas\noallgaps\example.091.AA.strNOG.ENOG411BWBU.fasta From 6e044c3fd06323d7ea4ddcda3567854ea51fa278 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 11:17:37 +0200 Subject: [PATCH 49/61] Delete scripts/generate_trimmed_msas_Windows.sh --- scripts/generate_trimmed_msas_Windows.sh | 512 ----------------------- 1 file changed, 512 deletions(-) delete mode 100644 scripts/generate_trimmed_msas_Windows.sh diff --git a/scripts/generate_trimmed_msas_Windows.sh b/scripts/generate_trimmed_msas_Windows.sh deleted file mode 100644 index cba5b3ed2..000000000 --- a/scripts/generate_trimmed_msas_Windows.sh +++ /dev/null @@ -1,512 +0,0 @@ -mkdir test_msas -mkdir test_msas/gappyout -mkdir test_msas/strict -mkdir test_msas/strictplus -mkdir test_msas/automated1 -mkdir test_msas/nogaps -mkdir test_msas/noallgaps - -./source/trimal.exe -in dataset/example.004.AA.fasta -gappyout > test_msas/gappyout/example.004.AA.fasta -./source/trimal.exe -in dataset/example.004.AA.fasta -strict > test_msas/strict/example.004.AA.fasta -./source/trimal.exe -in dataset/example.004.AA.fasta -strictplus > test_msas/strictplus/example.004.AA.fasta -./source/trimal.exe -in dataset/example.004.AA.fasta -automated1 > test_msas/automated1/example.004.AA.fasta -./source/trimal.exe -in dataset/example.004.AA.fasta -nogaps > test_msas/nogaps/example.004.AA.fasta -./source/trimal.exe -in dataset/example.004.AA.fasta -noallgaps > test_msas/noallgaps/example.004.AA.fasta -./source/trimal.exe -in dataset/example.005.AA.fasta -gappyout > test_msas/gappyout/example.005.AA.fasta -./source/trimal.exe -in dataset/example.005.AA.fasta -strict > test_msas/strict/example.005.AA.fasta -./source/trimal.exe -in dataset/example.005.AA.fasta -strictplus > test_msas/strictplus/example.005.AA.fasta -./source/trimal.exe -in dataset/example.005.AA.fasta -automated1 > test_msas/automated1/example.005.AA.fasta -./source/trimal.exe -in dataset/example.005.AA.fasta -nogaps > test_msas/nogaps/example.005.AA.fasta -./source/trimal.exe -in dataset/example.005.AA.fasta -noallgaps > test_msas/noallgaps/example.005.AA.fasta -./source/trimal.exe -in dataset/example.007.AA.fasta -gappyout > test_msas/gappyout/example.007.AA.fasta -./source/trimal.exe -in dataset/example.007.AA.fasta -strict > test_msas/strict/example.007.AA.fasta -./source/trimal.exe -in dataset/example.007.AA.fasta -strictplus > test_msas/strictplus/example.007.AA.fasta -./source/trimal.exe -in dataset/example.007.AA.fasta -automated1 > test_msas/automated1/example.007.AA.fasta -./source/trimal.exe -in dataset/example.007.AA.fasta -nogaps > test_msas/nogaps/example.007.AA.fasta -./source/trimal.exe -in dataset/example.007.AA.fasta -noallgaps > test_msas/noallgaps/example.007.AA.fasta -./source/trimal.exe -in dataset/example.009.AA.fasta -gappyout > test_msas/gappyout/example.009.AA.fasta -./source/trimal.exe -in dataset/example.009.AA.fasta -strict > test_msas/strict/example.009.AA.fasta -./source/trimal.exe -in dataset/example.009.AA.fasta -strictplus > test_msas/strictplus/example.009.AA.fasta -./source/trimal.exe -in dataset/example.009.AA.fasta -automated1 > test_msas/automated1/example.009.AA.fasta -./source/trimal.exe -in dataset/example.009.AA.fasta -nogaps > test_msas/nogaps/example.009.AA.fasta -./source/trimal.exe -in dataset/example.009.AA.fasta -noallgaps > test_msas/noallgaps/example.009.AA.fasta -./source/trimal.exe -in dataset/example.010.AA.fasta -gappyout > test_msas/gappyout/example.010.AA.fasta -./source/trimal.exe -in dataset/example.010.AA.fasta -strict > test_msas/strict/example.010.AA.fasta -./source/trimal.exe -in dataset/example.010.AA.fasta -strictplus > test_msas/strictplus/example.010.AA.fasta -./source/trimal.exe -in dataset/example.010.AA.fasta -automated1 > test_msas/automated1/example.010.AA.fasta -./source/trimal.exe -in dataset/example.010.AA.fasta -nogaps > test_msas/nogaps/example.010.AA.fasta -./source/trimal.exe -in dataset/example.010.AA.fasta -noallgaps > test_msas/noallgaps/example.010.AA.fasta -./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -gappyout > test_msas/gappyout/example.011.AA.YKL197C.fasta -./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -strict > test_msas/strict/example.011.AA.YKL197C.fasta -./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -strictplus > test_msas/strictplus/example.011.AA.YKL197C.fasta -./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -automated1 > test_msas/automated1/example.011.AA.YKL197C.fasta -./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -nogaps > test_msas/nogaps/example.011.AA.YKL197C.fasta -./source/trimal.exe -in dataset/example.011.AA.YKL197C.fasta -noallgaps > test_msas/noallgaps/example.011.AA.YKL197C.fasta -./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -gappyout > test_msas/gappyout/example.014.AA.EggNOG.COG0591.fasta -./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -strict > test_msas/strict/example.014.AA.EggNOG.COG0591.fasta -./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -strictplus > test_msas/strictplus/example.014.AA.EggNOG.COG0591.fasta -./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -automated1 > test_msas/automated1/example.014.AA.EggNOG.COG0591.fasta -./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -nogaps > test_msas/nogaps/example.014.AA.EggNOG.COG0591.fasta -./source/trimal.exe -in dataset/example.014.AA.EggNOG.COG0591.fasta -noallgaps > test_msas/noallgaps/example.014.AA.EggNOG.COG0591.fasta -./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -gappyout > test_msas/gappyout/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -strict > test_msas/strict/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -strictplus > test_msas/strictplus/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -automated1 > test_msas/automated1/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -nogaps > test_msas/nogaps/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal.exe -in dataset/example.015.AA.bctoNOG.ENOG41099F3.fasta -noallgaps > test_msas/noallgaps/example.015.AA.bctoNOG.ENOG41099F3.fasta -./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -gappyout > test_msas/gappyout/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -strict > test_msas/strict/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -strictplus > test_msas/strictplus/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -automated1 > test_msas/automated1/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -nogaps > test_msas/nogaps/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal.exe -in dataset/example.016.AA.bctoNOG.ENOG41099FB.fasta -noallgaps > test_msas/noallgaps/example.016.AA.bctoNOG.ENOG41099FB.fasta -./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -gappyout > test_msas/gappyout/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -strict > test_msas/strict/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -strictplus > test_msas/strictplus/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -automated1 > test_msas/automated1/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -nogaps > test_msas/nogaps/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal.exe -in dataset/example.017.AA.bctoNOG.ENOG41099FJ.fasta -noallgaps > test_msas/noallgaps/example.017.AA.bctoNOG.ENOG41099FJ.fasta -./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -gappyout > test_msas/gappyout/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -strict > test_msas/strict/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -strictplus > test_msas/strictplus/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -automated1 > test_msas/automated1/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -nogaps > test_msas/nogaps/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal.exe -in dataset/example.018.AA.bctoNOG.ENOG41099FV.fasta -noallgaps > test_msas/noallgaps/example.018.AA.bctoNOG.ENOG41099FV.fasta -./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -gappyout > test_msas/gappyout/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -strict > test_msas/strict/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -strictplus > test_msas/strictplus/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -automated1 > test_msas/automated1/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -nogaps > test_msas/nogaps/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal.exe -in dataset/example.019.AA.bctoNOG.ENOG41099HI.fasta -noallgaps > test_msas/noallgaps/example.019.AA.bctoNOG.ENOG41099HI.fasta -./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -gappyout > test_msas/gappyout/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -strict > test_msas/strict/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -strictplus > test_msas/strictplus/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -automated1 > test_msas/automated1/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -nogaps > test_msas/nogaps/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal.exe -in dataset/example.020.AA.bctoNOG.ENOG41099HN.fasta -noallgaps > test_msas/noallgaps/example.020.AA.bctoNOG.ENOG41099HN.fasta -./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -gappyout > test_msas/gappyout/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -strict > test_msas/strict/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -strictplus > test_msas/strictplus/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -automated1 > test_msas/automated1/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -nogaps > test_msas/nogaps/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal.exe -in dataset/example.021.AA.bctoNOG.ENOG41099I5.fasta -noallgaps > test_msas/noallgaps/example.021.AA.bctoNOG.ENOG41099I5.fasta -./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -gappyout > test_msas/gappyout/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -strict > test_msas/strict/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -strictplus > test_msas/strictplus/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -automated1 > test_msas/automated1/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -nogaps > test_msas/nogaps/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal.exe -in dataset/example.022.AA.bctoNOG.ENOG41099IZ.fasta -noallgaps > test_msas/noallgaps/example.022.AA.bctoNOG.ENOG41099IZ.fasta -./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -gappyout > test_msas/gappyout/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -strict > test_msas/strict/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -strictplus > test_msas/strictplus/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -automated1 > test_msas/automated1/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -nogaps > test_msas/nogaps/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal.exe -in dataset/example.023.AA.bctoNOG.ENOG41099K3.fasta -noallgaps > test_msas/noallgaps/example.023.AA.bctoNOG.ENOG41099K3.fasta -./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -gappyout > test_msas/gappyout/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -strict > test_msas/strict/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -strictplus > test_msas/strictplus/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -automated1 > test_msas/automated1/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -nogaps > test_msas/nogaps/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal.exe -in dataset/example.024.AA.bctoNOG.ENOG41099KM.fasta -noallgaps > test_msas/noallgaps/example.024.AA.bctoNOG.ENOG41099KM.fasta -./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -gappyout > test_msas/gappyout/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -strict > test_msas/strict/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -strictplus > test_msas/strictplus/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -automated1 > test_msas/automated1/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -nogaps > test_msas/nogaps/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal.exe -in dataset/example.025.AA.bctoNOG.ENOG41099KP.fasta -noallgaps > test_msas/noallgaps/example.025.AA.bctoNOG.ENOG41099KP.fasta -./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -gappyout > test_msas/gappyout/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -strict > test_msas/strict/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -strictplus > test_msas/strictplus/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -automated1 > test_msas/automated1/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -nogaps > test_msas/nogaps/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal.exe -in dataset/example.026.AA.bctoNOG.ENOG41099MV.fasta -noallgaps > test_msas/noallgaps/example.026.AA.bctoNOG.ENOG41099MV.fasta -./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -gappyout > test_msas/gappyout/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -strict > test_msas/strict/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -strictplus > test_msas/strictplus/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -automated1 > test_msas/automated1/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -nogaps > test_msas/nogaps/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal.exe -in dataset/example.027.AA.bctoNOG.ENOG41099NY.fasta -noallgaps > test_msas/noallgaps/example.027.AA.bctoNOG.ENOG41099NY.fasta -./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -gappyout > test_msas/gappyout/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -strict > test_msas/strict/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -strictplus > test_msas/strictplus/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -automated1 > test_msas/automated1/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -nogaps > test_msas/nogaps/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal.exe -in dataset/example.028.AA.bctoNOG.ENOG41099PA.fasta -noallgaps > test_msas/noallgaps/example.028.AA.bctoNOG.ENOG41099PA.fasta -./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -gappyout > test_msas/gappyout/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -strict > test_msas/strict/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -strictplus > test_msas/strictplus/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -automated1 > test_msas/automated1/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -nogaps > test_msas/nogaps/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal.exe -in dataset/example.029.AA.bctoNOG.ENOG41099Q3.fasta -noallgaps > test_msas/noallgaps/example.029.AA.bctoNOG.ENOG41099Q3.fasta -./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -gappyout > test_msas/gappyout/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -strict > test_msas/strict/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -strictplus > test_msas/strictplus/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -automated1 > test_msas/automated1/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -nogaps > test_msas/nogaps/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal.exe -in dataset/example.030.AA.bctoNOG.ENOG41099RG.fasta -noallgaps > test_msas/noallgaps/example.030.AA.bctoNOG.ENOG41099RG.fasta -./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -gappyout > test_msas/gappyout/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -strict > test_msas/strict/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -strictplus > test_msas/strictplus/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -automated1 > test_msas/automated1/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -nogaps > test_msas/nogaps/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal.exe -in dataset/example.031.AA.bctoNOG.ENOG41099UK.fasta -noallgaps > test_msas/noallgaps/example.031.AA.bctoNOG.ENOG41099UK.fasta -./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -gappyout > test_msas/gappyout/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -strict > test_msas/strict/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -strictplus > test_msas/strictplus/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -automated1 > test_msas/automated1/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -nogaps > test_msas/nogaps/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal.exe -in dataset/example.032.AA.bctoNOG.ENOG41099UW.fasta -noallgaps > test_msas/noallgaps/example.032.AA.bctoNOG.ENOG41099UW.fasta -./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -gappyout > test_msas/gappyout/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -strict > test_msas/strict/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -strictplus > test_msas/strictplus/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -automated1 > test_msas/automated1/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -nogaps > test_msas/nogaps/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal.exe -in dataset/example.033.AA.bctoNOG.ENOG41099VK.fasta -noallgaps > test_msas/noallgaps/example.033.AA.bctoNOG.ENOG41099VK.fasta -./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -gappyout > test_msas/gappyout/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -strict > test_msas/strict/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -strictplus > test_msas/strictplus/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -automated1 > test_msas/automated1/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -nogaps > test_msas/nogaps/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal.exe -in dataset/example.034.AA.bctoNOG.ENOG41099WA.fasta -noallgaps > test_msas/noallgaps/example.034.AA.bctoNOG.ENOG41099WA.fasta -./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -gappyout > test_msas/gappyout/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -strict > test_msas/strict/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -strictplus > test_msas/strictplus/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -automated1 > test_msas/automated1/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -nogaps > test_msas/nogaps/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal.exe -in dataset/example.035.AA.bctoNOG.ENOG41099WF.fasta -noallgaps > test_msas/noallgaps/example.035.AA.bctoNOG.ENOG41099WF.fasta -./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -gappyout > test_msas/gappyout/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -strict > test_msas/strict/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -strictplus > test_msas/strictplus/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -automated1 > test_msas/automated1/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -nogaps > test_msas/nogaps/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal.exe -in dataset/example.036.AA.bctoNOG.ENOG41099XJ.fasta -noallgaps > test_msas/noallgaps/example.036.AA.bctoNOG.ENOG41099XJ.fasta -./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -gappyout > test_msas/gappyout/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -strict > test_msas/strict/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -strictplus > test_msas/strictplus/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -automated1 > test_msas/automated1/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -nogaps > test_msas/nogaps/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal.exe -in dataset/example.037.AA.bctoNOG.ENOG41099XP.fasta -noallgaps > test_msas/noallgaps/example.037.AA.bctoNOG.ENOG41099XP.fasta -./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -gappyout > test_msas/gappyout/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -strict > test_msas/strict/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -strictplus > test_msas/strictplus/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -automated1 > test_msas/automated1/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -nogaps > test_msas/nogaps/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal.exe -in dataset/example.038.AA.bctoNOG.ENOG41099Y4.fasta -noallgaps > test_msas/noallgaps/example.038.AA.bctoNOG.ENOG41099Y4.fasta -./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -gappyout > test_msas/gappyout/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -strict > test_msas/strict/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -strictplus > test_msas/strictplus/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -automated1 > test_msas/automated1/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -nogaps > test_msas/nogaps/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal.exe -in dataset/example.039.AA.bctoNOG.ENOG41099YD.fasta -noallgaps > test_msas/noallgaps/example.039.AA.bctoNOG.ENOG41099YD.fasta -./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -gappyout > test_msas/gappyout/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -strict > test_msas/strict/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -strictplus > test_msas/strictplus/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -automated1 > test_msas/automated1/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -nogaps > test_msas/nogaps/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal.exe -in dataset/example.040.AA.bctoNOG.ENOG4109A32.fasta -noallgaps > test_msas/noallgaps/example.040.AA.bctoNOG.ENOG4109A32.fasta -./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -gappyout > test_msas/gappyout/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -strict > test_msas/strict/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -strictplus > test_msas/strictplus/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -automated1 > test_msas/automated1/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -nogaps > test_msas/nogaps/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal.exe -in dataset/example.041.AA.bctoNOG.ENOG4109A5T.fasta -noallgaps > test_msas/noallgaps/example.041.AA.bctoNOG.ENOG4109A5T.fasta -./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -gappyout > test_msas/gappyout/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -strict > test_msas/strict/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -strictplus > test_msas/strictplus/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -automated1 > test_msas/automated1/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -nogaps > test_msas/nogaps/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal.exe -in dataset/example.042.AA.bctoNOG.ENOG4109A9M.fasta -noallgaps > test_msas/noallgaps/example.042.AA.bctoNOG.ENOG4109A9M.fasta -./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -gappyout > test_msas/gappyout/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -strict > test_msas/strict/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -strictplus > test_msas/strictplus/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -automated1 > test_msas/automated1/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -nogaps > test_msas/nogaps/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal.exe -in dataset/example.043.AA.bctoNOG.ENOG4109ADN.fasta -noallgaps > test_msas/noallgaps/example.043.AA.bctoNOG.ENOG4109ADN.fasta -./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -gappyout > test_msas/gappyout/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -strict > test_msas/strict/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -strictplus > test_msas/strictplus/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -automated1 > test_msas/automated1/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -nogaps > test_msas/nogaps/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal.exe -in dataset/example.044.AA.bctoNOG.ENOG4109AED.fasta -noallgaps > test_msas/noallgaps/example.044.AA.bctoNOG.ENOG4109AED.fasta -./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -gappyout > test_msas/gappyout/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -strict > test_msas/strict/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -strictplus > test_msas/strictplus/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -automated1 > test_msas/automated1/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -nogaps > test_msas/nogaps/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal.exe -in dataset/example.045.AA.bctoNOG.ENOG4109AGT.fasta -noallgaps > test_msas/noallgaps/example.045.AA.bctoNOG.ENOG4109AGT.fasta -./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -gappyout > test_msas/gappyout/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -strict > test_msas/strict/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -strictplus > test_msas/strictplus/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -automated1 > test_msas/automated1/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -nogaps > test_msas/nogaps/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal.exe -in dataset/example.046.AA.bctoNOG.ENOG4109AGW.fasta -noallgaps > test_msas/noallgaps/example.046.AA.bctoNOG.ENOG4109AGW.fasta -./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -gappyout > test_msas/gappyout/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -strict > test_msas/strict/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -strictplus > test_msas/strictplus/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -automated1 > test_msas/automated1/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -nogaps > test_msas/nogaps/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal.exe -in dataset/example.047.AA.bctoNOG.ENOG4109AIC.fasta -noallgaps > test_msas/noallgaps/example.047.AA.bctoNOG.ENOG4109AIC.fasta -./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -gappyout > test_msas/gappyout/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strict > test_msas/strict/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -strictplus > test_msas/strictplus/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -automated1 > test_msas/automated1/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -nogaps > test_msas/nogaps/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal.exe -in dataset/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -noallgaps > test_msas/noallgaps/example.048.AA.bctoNOG.ENOG4109AJ3.fasta -./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -gappyout > test_msas/gappyout/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -strict > test_msas/strict/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -strictplus > test_msas/strictplus/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -automated1 > test_msas/automated1/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -nogaps > test_msas/nogaps/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal.exe -in dataset/example.049.AA.bctoNOG.ENOG4109AY5.fasta -noallgaps > test_msas/noallgaps/example.049.AA.bctoNOG.ENOG4109AY5.fasta -./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -gappyout > test_msas/gappyout/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strict > test_msas/strict/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -strictplus > test_msas/strictplus/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -automated1 > test_msas/automated1/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -nogaps > test_msas/nogaps/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal.exe -in dataset/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -noallgaps > test_msas/noallgaps/example.050.AA.bctoNOG.ENOG4109B8Z.fasta -./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -gappyout > test_msas/gappyout/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strict > test_msas/strict/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -strictplus > test_msas/strictplus/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -automated1 > test_msas/automated1/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -nogaps > test_msas/nogaps/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal.exe -in dataset/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -noallgaps > test_msas/noallgaps/example.051.AA.bctoNOG.ENOG4109BCJ.fasta -./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -gappyout > test_msas/gappyout/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -strict > test_msas/strict/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -strictplus > test_msas/strictplus/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -automated1 > test_msas/automated1/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -nogaps > test_msas/nogaps/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal.exe -in dataset/example.052.AA.bctoNOG.ENOG4109CTU.fasta -noallgaps > test_msas/noallgaps/example.052.AA.bctoNOG.ENOG4109CTU.fasta -./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -gappyout > test_msas/gappyout/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -strict > test_msas/strict/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -strictplus > test_msas/strictplus/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -automated1 > test_msas/automated1/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -nogaps > test_msas/nogaps/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal.exe -in dataset/example.053.AA.bctoNOG.ENOG4109CVC.fasta -noallgaps > test_msas/noallgaps/example.053.AA.bctoNOG.ENOG4109CVC.fasta -./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -gappyout > test_msas/gappyout/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -strict > test_msas/strict/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -strictplus > test_msas/strictplus/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -automated1 > test_msas/automated1/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -nogaps > test_msas/nogaps/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal.exe -in dataset/example.054.AA.bctoNOG.ENOG4109FIT.fasta -noallgaps > test_msas/noallgaps/example.054.AA.bctoNOG.ENOG4109FIT.fasta -./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -gappyout > test_msas/gappyout/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -strict > test_msas/strict/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -strictplus > test_msas/strictplus/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -automated1 > test_msas/automated1/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -nogaps > test_msas/nogaps/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal.exe -in dataset/example.055.AA.bctoNOG.ENOG4109GY9.fasta -noallgaps > test_msas/noallgaps/example.055.AA.bctoNOG.ENOG4109GY9.fasta -./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -gappyout > test_msas/gappyout/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strict > test_msas/strict/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -strictplus > test_msas/strictplus/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -automated1 > test_msas/automated1/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -nogaps > test_msas/nogaps/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal.exe -in dataset/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -noallgaps > test_msas/noallgaps/example.056.AA.bctoNOG.ENOG4109IPJ.fasta -./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -gappyout > test_msas/gappyout/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strict > test_msas/strict/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -strictplus > test_msas/strictplus/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -automated1 > test_msas/automated1/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -nogaps > test_msas/nogaps/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal.exe -in dataset/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -noallgaps > test_msas/noallgaps/example.057.AA.bctoNOG.ENOG4109SZ2.fasta -./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -gappyout > test_msas/gappyout/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -strict > test_msas/strict/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -strictplus > test_msas/strictplus/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -automated1 > test_msas/automated1/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -nogaps > test_msas/nogaps/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal.exe -in dataset/example.058.AA.strNOG.ENOG411BBR6.fasta -noallgaps > test_msas/noallgaps/example.058.AA.strNOG.ENOG411BBR6.fasta -./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -gappyout > test_msas/gappyout/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -strict > test_msas/strict/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -strictplus > test_msas/strictplus/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -automated1 > test_msas/automated1/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -nogaps > test_msas/nogaps/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal.exe -in dataset/example.059.AA.strNOG.ENOG411BBRR.fasta -noallgaps > test_msas/noallgaps/example.059.AA.strNOG.ENOG411BBRR.fasta -./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -gappyout > test_msas/gappyout/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -strict > test_msas/strict/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -strictplus > test_msas/strictplus/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -automated1 > test_msas/automated1/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -nogaps > test_msas/nogaps/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal.exe -in dataset/example.060.AA.strNOG.ENOG411BBWK.fasta -noallgaps > test_msas/noallgaps/example.060.AA.strNOG.ENOG411BBWK.fasta -./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -gappyout > test_msas/gappyout/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -strict > test_msas/strict/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -strictplus > test_msas/strictplus/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -automated1 > test_msas/automated1/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -nogaps > test_msas/nogaps/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal.exe -in dataset/example.061.AA.strNOG.ENOG411BCDZ.fasta -noallgaps > test_msas/noallgaps/example.061.AA.strNOG.ENOG411BCDZ.fasta -./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -gappyout > test_msas/gappyout/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -strict > test_msas/strict/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -strictplus > test_msas/strictplus/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -automated1 > test_msas/automated1/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -nogaps > test_msas/nogaps/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal.exe -in dataset/example.062.AA.strNOG.ENOG411BCX3.fasta -noallgaps > test_msas/noallgaps/example.062.AA.strNOG.ENOG411BCX3.fasta -./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -gappyout > test_msas/gappyout/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -strict > test_msas/strict/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -strictplus > test_msas/strictplus/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -automated1 > test_msas/automated1/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -nogaps > test_msas/nogaps/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal.exe -in dataset/example.063.AA.strNOG.ENOG411BDBU.fasta -noallgaps > test_msas/noallgaps/example.063.AA.strNOG.ENOG411BDBU.fasta -./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -gappyout > test_msas/gappyout/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -strict > test_msas/strict/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -strictplus > test_msas/strictplus/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -automated1 > test_msas/automated1/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -nogaps > test_msas/nogaps/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal.exe -in dataset/example.064.AA.strNOG.ENOG411BDKC.fasta -noallgaps > test_msas/noallgaps/example.064.AA.strNOG.ENOG411BDKC.fasta -./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -gappyout > test_msas/gappyout/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -strict > test_msas/strict/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -strictplus > test_msas/strictplus/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -automated1 > test_msas/automated1/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -nogaps > test_msas/nogaps/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal.exe -in dataset/example.065.AA.strNOG.ENOG411BDSZ.fasta -noallgaps > test_msas/noallgaps/example.065.AA.strNOG.ENOG411BDSZ.fasta -./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -gappyout > test_msas/gappyout/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -strict > test_msas/strict/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -strictplus > test_msas/strictplus/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -automated1 > test_msas/automated1/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -nogaps > test_msas/nogaps/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal.exe -in dataset/example.066.AA.strNOG.ENOG411BDUE.fasta -noallgaps > test_msas/noallgaps/example.066.AA.strNOG.ENOG411BDUE.fasta -./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -gappyout > test_msas/gappyout/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -strict > test_msas/strict/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -strictplus > test_msas/strictplus/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -automated1 > test_msas/automated1/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -nogaps > test_msas/nogaps/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal.exe -in dataset/example.067.AA.strNOG.ENOG411BDX3.fasta -noallgaps > test_msas/noallgaps/example.067.AA.strNOG.ENOG411BDX3.fasta -./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -gappyout > test_msas/gappyout/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -strict > test_msas/strict/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -strictplus > test_msas/strictplus/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -automated1 > test_msas/automated1/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -nogaps > test_msas/nogaps/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal.exe -in dataset/example.068.AA.strNOG.ENOG411BE45.fasta -noallgaps > test_msas/noallgaps/example.068.AA.strNOG.ENOG411BE45.fasta -./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -gappyout > test_msas/gappyout/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -strict > test_msas/strict/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -strictplus > test_msas/strictplus/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -automated1 > test_msas/automated1/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -nogaps > test_msas/nogaps/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal.exe -in dataset/example.069.AA.strNOG.ENOG411BE8B.fasta -noallgaps > test_msas/noallgaps/example.069.AA.strNOG.ENOG411BE8B.fasta -./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -gappyout > test_msas/gappyout/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -strict > test_msas/strict/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -strictplus > test_msas/strictplus/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -automated1 > test_msas/automated1/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -nogaps > test_msas/nogaps/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal.exe -in dataset/example.070.AA.strNOG.ENOG411BEUV.fasta -noallgaps > test_msas/noallgaps/example.070.AA.strNOG.ENOG411BEUV.fasta -./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -gappyout > test_msas/gappyout/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -strict > test_msas/strict/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -strictplus > test_msas/strictplus/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -automated1 > test_msas/automated1/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -nogaps > test_msas/nogaps/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal.exe -in dataset/example.071.AA.strNOG.ENOG411BEZ0.fasta -noallgaps > test_msas/noallgaps/example.071.AA.strNOG.ENOG411BEZ0.fasta -./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -gappyout > test_msas/gappyout/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -strict > test_msas/strict/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -strictplus > test_msas/strictplus/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -automated1 > test_msas/automated1/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -nogaps > test_msas/nogaps/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal.exe -in dataset/example.072.AA.strNOG.ENOG411BF1S.fasta -noallgaps > test_msas/noallgaps/example.072.AA.strNOG.ENOG411BF1S.fasta -./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -gappyout > test_msas/gappyout/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -strict > test_msas/strict/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -strictplus > test_msas/strictplus/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -automated1 > test_msas/automated1/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -nogaps > test_msas/nogaps/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal.exe -in dataset/example.073.AA.strNOG.ENOG411BFCW.fasta -noallgaps > test_msas/noallgaps/example.073.AA.strNOG.ENOG411BFCW.fasta -./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -gappyout > test_msas/gappyout/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -strict > test_msas/strict/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -strictplus > test_msas/strictplus/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -automated1 > test_msas/automated1/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -nogaps > test_msas/nogaps/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal.exe -in dataset/example.074.AA.strNOG.ENOG411BFPF.fasta -noallgaps > test_msas/noallgaps/example.074.AA.strNOG.ENOG411BFPF.fasta -./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -gappyout > test_msas/gappyout/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -strict > test_msas/strict/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -strictplus > test_msas/strictplus/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -automated1 > test_msas/automated1/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -nogaps > test_msas/nogaps/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal.exe -in dataset/example.075.AA.strNOG.ENOG411BFQS.fasta -noallgaps > test_msas/noallgaps/example.075.AA.strNOG.ENOG411BFQS.fasta -./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -gappyout > test_msas/gappyout/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -strict > test_msas/strict/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -strictplus > test_msas/strictplus/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -automated1 > test_msas/automated1/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -nogaps > test_msas/nogaps/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal.exe -in dataset/example.076.AA.strNOG.ENOG411BH75.fasta -noallgaps > test_msas/noallgaps/example.076.AA.strNOG.ENOG411BH75.fasta -./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -gappyout > test_msas/gappyout/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -strict > test_msas/strict/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -strictplus > test_msas/strictplus/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -automated1 > test_msas/automated1/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -nogaps > test_msas/nogaps/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal.exe -in dataset/example.077.AA.strNOG.ENOG411BH79.fasta -noallgaps > test_msas/noallgaps/example.077.AA.strNOG.ENOG411BH79.fasta -./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -gappyout > test_msas/gappyout/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -strict > test_msas/strict/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -strictplus > test_msas/strictplus/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -automated1 > test_msas/automated1/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -nogaps > test_msas/nogaps/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal.exe -in dataset/example.078.AA.strNOG.ENOG411BH99.fasta -noallgaps > test_msas/noallgaps/example.078.AA.strNOG.ENOG411BH99.fasta -./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -gappyout > test_msas/gappyout/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -strict > test_msas/strict/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -strictplus > test_msas/strictplus/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -automated1 > test_msas/automated1/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -nogaps > test_msas/nogaps/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal.exe -in dataset/example.079.AA.strNOG.ENOG411BJDC.fasta -noallgaps > test_msas/noallgaps/example.079.AA.strNOG.ENOG411BJDC.fasta -./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -gappyout > test_msas/gappyout/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -strict > test_msas/strict/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -strictplus > test_msas/strictplus/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -automated1 > test_msas/automated1/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -nogaps > test_msas/nogaps/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal.exe -in dataset/example.080.AA.strNOG.ENOG411BJIF.fasta -noallgaps > test_msas/noallgaps/example.080.AA.strNOG.ENOG411BJIF.fasta -./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -gappyout > test_msas/gappyout/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -strict > test_msas/strict/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -strictplus > test_msas/strictplus/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -automated1 > test_msas/automated1/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -nogaps > test_msas/nogaps/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal.exe -in dataset/example.081.AA.strNOG.ENOG411BK9X.fasta -noallgaps > test_msas/noallgaps/example.081.AA.strNOG.ENOG411BK9X.fasta -./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -gappyout > test_msas/gappyout/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -strict > test_msas/strict/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -strictplus > test_msas/strictplus/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -automated1 > test_msas/automated1/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -nogaps > test_msas/nogaps/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal.exe -in dataset/example.082.AA.strNOG.ENOG411BKC5.fasta -noallgaps > test_msas/noallgaps/example.082.AA.strNOG.ENOG411BKC5.fasta -./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -gappyout > test_msas/gappyout/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -strict > test_msas/strict/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -strictplus > test_msas/strictplus/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -automated1 > test_msas/automated1/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -nogaps > test_msas/nogaps/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal.exe -in dataset/example.083.AA.strNOG.ENOG411BMKC.fasta -noallgaps > test_msas/noallgaps/example.083.AA.strNOG.ENOG411BMKC.fasta -./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -gappyout > test_msas/gappyout/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -strict > test_msas/strict/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -strictplus > test_msas/strictplus/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -automated1 > test_msas/automated1/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -nogaps > test_msas/nogaps/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal.exe -in dataset/example.084.AA.strNOG.ENOG411BNP9.fasta -noallgaps > test_msas/noallgaps/example.084.AA.strNOG.ENOG411BNP9.fasta -./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -gappyout > test_msas/gappyout/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -strict > test_msas/strict/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -strictplus > test_msas/strictplus/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -automated1 > test_msas/automated1/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -nogaps > test_msas/nogaps/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal.exe -in dataset/example.085.AA.strNOG.ENOG411BQTJ.fasta -noallgaps > test_msas/noallgaps/example.085.AA.strNOG.ENOG411BQTJ.fasta -./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -gappyout > test_msas/gappyout/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -strict > test_msas/strict/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -strictplus > test_msas/strictplus/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -automated1 > test_msas/automated1/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -nogaps > test_msas/nogaps/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal.exe -in dataset/example.086.AA.strNOG.ENOG411BR1D.fasta -noallgaps > test_msas/noallgaps/example.086.AA.strNOG.ENOG411BR1D.fasta -./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -gappyout > test_msas/gappyout/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -strict > test_msas/strict/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -strictplus > test_msas/strictplus/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -automated1 > test_msas/automated1/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -nogaps > test_msas/nogaps/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal.exe -in dataset/example.087.AA.strNOG.ENOG411BRCH.fasta -noallgaps > test_msas/noallgaps/example.087.AA.strNOG.ENOG411BRCH.fasta -./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -gappyout > test_msas/gappyout/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -strict > test_msas/strict/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -strictplus > test_msas/strictplus/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -automated1 > test_msas/automated1/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -nogaps > test_msas/nogaps/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal.exe -in dataset/example.088.AA.strNOG.ENOG411BSXF.fasta -noallgaps > test_msas/noallgaps/example.088.AA.strNOG.ENOG411BSXF.fasta -./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -gappyout > test_msas/gappyout/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -strict > test_msas/strict/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -strictplus > test_msas/strictplus/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -automated1 > test_msas/automated1/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -nogaps > test_msas/nogaps/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal.exe -in dataset/example.089.AA.strNOG.ENOG411BV9B.fasta -noallgaps > test_msas/noallgaps/example.089.AA.strNOG.ENOG411BV9B.fasta -./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -gappyout > test_msas/gappyout/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -strict > test_msas/strict/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -strictplus > test_msas/strictplus/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -automated1 > test_msas/automated1/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -nogaps > test_msas/nogaps/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal.exe -in dataset/example.090.AA.strNOG.ENOG411BVKR.fasta -noallgaps > test_msas/noallgaps/example.090.AA.strNOG.ENOG411BVKR.fasta -./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -gappyout > test_msas/gappyout/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -strict > test_msas/strict/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -strictplus > test_msas/strictplus/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -automated1 > test_msas/automated1/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -nogaps > test_msas/nogaps/example.091.AA.strNOG.ENOG411BWBU.fasta -./source/trimal.exe -in dataset/example.091.AA.strNOG.ENOG411BWBU.fasta -noallgaps > test_msas/noallgaps/example.091.AA.strNOG.ENOG411BWBU.fasta From 9b420c6e421ca22a77fd6ed78eaab415b2b4c2e8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 11:22:32 +0200 Subject: [PATCH 50/61] Add download release tests --- .github/workflows/build.yml | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 5e983aed5..7cfd89044 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -13,6 +13,30 @@ on: name: Build jobs: + download_and_test_windows: + runs-on: windows-2022 + steps: + - uses: actions/checkout@v4 + - name: Download Release Binaries + run: | + curl -L -o trimal.zip https://github.com/inab/trimal/releases/download/v1.5.0/trimAl_Windows_x86-64.zip + + - name: Unzip Binaries + run: | + powershell -Command "Expand-Archive -Path trimal.zip -DestinationPath ." + + - name: Verify Binaries + run: | + Move-Item -Path .\trimal.exe -Destination .\source\ + Get-Command .\source\trimal.exe + + - name: Run generate_trimmed_msas.ps1 + run: | + powershell -ExecutionPolicy Bypass -File .\scripts\generate_trimmed_msas.ps1 + + - name: Run compare_trimmed_msas.ps1 + run: | + powershell -ExecutionPolicy Bypass -File .\scripts\compare_trimmed_msas.ps1 build_and_test_windows: runs-on: windows-2022 steps: From f5388e9eb69248ea0c901c73d9d56acb035034c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 11:22:42 +0200 Subject: [PATCH 51/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 30096e3de..1f9a8f15a 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched +Temporary file to force Github Actions workflow to be launched. From e613fa85819807db35ad88257366cda1745b7533 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 11:47:36 +0200 Subject: [PATCH 52/61] Add Linux tests --- .github/workflows/build.yml | 64 +++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 7cfd89044..a0ee9a549 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -13,6 +13,69 @@ on: name: Build jobs: + download_and_test_ubuntu: + runs-on: ubuntu-20.04 + strategy: + matrix: + arch: [x86_64, aarch64] + + steps: + - uses: actions/checkout@v4 + - name: Download Release Binaries + run: | + curl -L -o trimal.zip https://github.com/inab/trimal/releases/download/v1.5.0/trimAl_Linux_x86-64.zip + - name: Test trimal for Linux x86_64 + if: matrix.arch == 'x86_64' + run: unzip trimAl_Linux_x86-64.zip && mv trimAl_Linux_x86-64/* source/ && file source/trimal && + file source/readal && file source/statal && ./scripts/generate_trimmed_msas.sh && + ./scripts/compare_trimmed_msas.sh + + - name: Build trimal for Linux aarch64 + if: matrix.arch == 'aarch64' + uses: uraimo/run-on-arch-action@v2 + with: + arch: ${{ matrix.arch }} + distro: ubuntu20.04 + githubToken: ${{ github.token }} + dockerRunArgs: | + --volume "${PWD}:/trimal" + install: | + apt-get update -q -y + apt-get install -q -y file + run: | + curl -L -o trimal.zip https://github.com/inab/trimal/releases/download/v1.5.0/trimAl_Linux_x86-64.zip && + unzip trimAl_Linux_x86-64.zip && mv trimAl_Linux_x86-64/* source/ && file source/trimal && + file source/readal && file source/statal && ./scripts/generate_trimmed_msas.sh && + ./scripts/compare_trimmed_msas.sh + build_and_test_ubuntu: + runs-on: ubuntu-20.04 + strategy: + matrix: + arch: [x86_64, aarch64] + + steps: + - uses: actions/checkout@v4 + - name: Build trimal for Linux x86_64 + if: matrix.arch == 'x86_64' + run: cd source && make all && file trimal && file readal && file statal && + cd .. && ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh + + - name: Build trimal for Linux aarch64 + if: matrix.arch == 'aarch64' + uses: uraimo/run-on-arch-action@v2 + with: + arch: ${{ matrix.arch }} + distro: ubuntu20.04 + githubToken: ${{ github.token }} + dockerRunArgs: | + --volume "${PWD}:/trimal" + install: | + apt-get update -q -y + apt-get install -q -y make g++ file + run: | + cd /trimal/source && make all && file trimal && file readal && file statal && + cd .. && ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh + download_and_test_windows: runs-on: windows-2022 steps: @@ -37,6 +100,7 @@ jobs: - name: Run compare_trimmed_msas.ps1 run: | powershell -ExecutionPolicy Bypass -File .\scripts\compare_trimmed_msas.ps1 + build_and_test_windows: runs-on: windows-2022 steps: From c4e90057c26fd7742b5410d9aa491d46e4e7674a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 11:47:48 +0200 Subject: [PATCH 53/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 1f9a8f15a..30096e3de 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched. +Temporary file to force Github Actions workflow to be launched From 13954c5219648b452177af5e511a4d3b4b298700 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 12:57:09 +0200 Subject: [PATCH 54/61] Update build.yml --- .github/workflows/build.yml | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index a0ee9a549..f348f2f57 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -23,11 +23,11 @@ jobs: - uses: actions/checkout@v4 - name: Download Release Binaries run: | - curl -L -o trimal.zip https://github.com/inab/trimal/releases/download/v1.5.0/trimAl_Linux_x86-64.zip + curl -L -o trimal.zip https://github.com/inab/trimal/releases/download/v1.5.0/trimAl_Linux_x86-64.zip && + unzip trimal.zip && mv trimal/* source/ - name: Test trimal for Linux x86_64 if: matrix.arch == 'x86_64' - run: unzip trimAl_Linux_x86-64.zip && mv trimAl_Linux_x86-64/* source/ && file source/trimal && - file source/readal && file source/statal && ./scripts/generate_trimmed_msas.sh && + run: file source/trimal && file source/readal && file source/statal && ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh - name: Build trimal for Linux aarch64 @@ -43,9 +43,7 @@ jobs: apt-get update -q -y apt-get install -q -y file run: | - curl -L -o trimal.zip https://github.com/inab/trimal/releases/download/v1.5.0/trimAl_Linux_x86-64.zip && - unzip trimAl_Linux_x86-64.zip && mv trimAl_Linux_x86-64/* source/ && file source/trimal && - file source/readal && file source/statal && ./scripts/generate_trimmed_msas.sh && + file source/trimal && file source/readal && file source/statal && ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh build_and_test_ubuntu: runs-on: ubuntu-20.04 From bd2e5d3741cc459bae00b6dc47cd4c09680e9d34 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 12:57:25 +0200 Subject: [PATCH 55/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 30096e3de..1f9a8f15a 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched +Temporary file to force Github Actions workflow to be launched. From bf2e0013bb557d5580b24eee5f80b0419aa107aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 13:00:18 +0200 Subject: [PATCH 56/61] Fix folder name --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index f348f2f57..9071ec668 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -24,7 +24,7 @@ jobs: - name: Download Release Binaries run: | curl -L -o trimal.zip https://github.com/inab/trimal/releases/download/v1.5.0/trimAl_Linux_x86-64.zip && - unzip trimal.zip && mv trimal/* source/ + unzip trimal.zip && mv trimAl_Linux_x86-64/* source/ - name: Test trimal for Linux x86_64 if: matrix.arch == 'x86_64' run: file source/trimal && file source/readal && file source/statal && ./scripts/generate_trimmed_msas.sh && From 702b924057fc583005bd610eaa111e9c46189ef4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 13:00:30 +0200 Subject: [PATCH 57/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 1f9a8f15a..30096e3de 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched. +Temporary file to force Github Actions workflow to be launched From a4e2704db3a2de923aa2239ba72b5319d98f97da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 13:09:50 +0200 Subject: [PATCH 58/61] Ignore arch64 download release --- .github/workflows/build.yml | 22 +--------------------- 1 file changed, 1 insertion(+), 21 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 9071ec668..cfd5436da 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -15,10 +15,6 @@ name: Build jobs: download_and_test_ubuntu: runs-on: ubuntu-20.04 - strategy: - matrix: - arch: [x86_64, aarch64] - steps: - uses: actions/checkout@v4 - name: Download Release Binaries @@ -26,25 +22,9 @@ jobs: curl -L -o trimal.zip https://github.com/inab/trimal/releases/download/v1.5.0/trimAl_Linux_x86-64.zip && unzip trimal.zip && mv trimAl_Linux_x86-64/* source/ - name: Test trimal for Linux x86_64 - if: matrix.arch == 'x86_64' run: file source/trimal && file source/readal && file source/statal && ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh - - - name: Build trimal for Linux aarch64 - if: matrix.arch == 'aarch64' - uses: uraimo/run-on-arch-action@v2 - with: - arch: ${{ matrix.arch }} - distro: ubuntu20.04 - githubToken: ${{ github.token }} - dockerRunArgs: | - --volume "${PWD}:/trimal" - install: | - apt-get update -q -y - apt-get install -q -y file - run: | - file source/trimal && file source/readal && file source/statal && ./scripts/generate_trimmed_msas.sh && - ./scripts/compare_trimmed_msas.sh + build_and_test_ubuntu: runs-on: ubuntu-20.04 strategy: From e7ca094df26f103d3478ba9cd9bc35a8adae626b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Mon, 12 Aug 2024 13:10:14 +0200 Subject: [PATCH 59/61] Edit file to force workflow run --- scripts/dummy-file.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt index 30096e3de..1f9a8f15a 100644 --- a/scripts/dummy-file.txt +++ b/scripts/dummy-file.txt @@ -1 +1 @@ -Temporary file to force Github Actions workflow to be launched +Temporary file to force Github Actions workflow to be launched. From 8b1ca559afa25d6a2559af6c7b15da79867159e2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 25 Sep 2024 11:16:07 +0200 Subject: [PATCH 60/61] Update .gitignore --- .gitignore | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 420652414..38ce5d5b1 100644 --- a/.gitignore +++ b/.gitignore @@ -2,4 +2,5 @@ source/readal source/statal source/trimal -docs/build \ No newline at end of file +docs/build +scripts/dummy-file.txt From ba2668249ea357096be65a85fff2ddf9b445124e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= <46527244+nicodr97@users.noreply.github.com> Date: Wed, 25 Sep 2024 11:17:55 +0200 Subject: [PATCH 61/61] Delete scripts/dummy-file.txt --- scripts/dummy-file.txt | 1 - 1 file changed, 1 deletion(-) delete mode 100644 scripts/dummy-file.txt diff --git a/scripts/dummy-file.txt b/scripts/dummy-file.txt deleted file mode 100644 index 1f9a8f15a..000000000 --- a/scripts/dummy-file.txt +++ /dev/null @@ -1 +0,0 @@ -Temporary file to force Github Actions workflow to be launched.