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Mark v1.4 and v2 parameters
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@nicodr97
nicodr97 committed Jan 26, 2024
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176 changes: 92 additions & 84 deletions docs/source/usage.rst
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Usage
***********************

Here we show all the options that trimAl offers to the user. Some parameters are only available on v2. At the bottom there are some examples of how to use the tool.

Basic usage
=================
::
Expand All @@ -10,15 +12,15 @@ Basic usage

Help Options
=================
.. option:: --help
.. option:: -h

Print this information and show some examples.

.. option:: --version

Print the trimAl version.

.. option:: -v <level>, --verbose <level>
.. option:: -v <level>, --verbose <level> (v2)

Specify the verbose level of the program.
Available options: error / 3, warning / 2, info / 1, none / 0
Expand All @@ -29,15 +31,19 @@ Input-Output Options
.. option:: -in <inputfile>

Input file in several formats.
Available input formats: clustal, fasta, mega_interleaved, mega_sequential, nexus, phylip32, phylip40, phylip_paml, pir
Available input formats: clustal, fasta, mega_interleaved (v2), mega_sequential (v2), nexus, phylip32, phylip40, phylip_paml (v2), pir

.. option:: -formats <format1,...>
.. option:: -formats <format1,...> (v2)

Specify one or more formats to save the resulting MSA. Separated by spaces
Combinations with specific format arguments (-fasta, -nexus, etc) is allowed.
Available output formats: clustal, fasta_m10, fasta, html, mega_sequential, nexus_m10, nexus, phylip32_m10, phylip32, phylip40_m10, phylip40, phylip_paml_m10, phylip_paml, pir

.. option:: -out <outputfile>

.. option:: -out <outputfile> (v1.4)

Output alignment in the same input format (default stdout).

.. option:: -out <outputfile> (v2)

Output path pattern. (default stdout).

Expand Down Expand Up @@ -76,22 +82,80 @@ Input-Output Options
trimal -in file1.fasta -out ./[in]/trimmed.[format] -formats fasta
-> ./file1/trimmed.fasta (ONLY if folder file1 already exists)

.. option:: -lf, --listformats
.. option:: -lf, --listformats (v2)

List available formats to load from and save to.
List available formats to load from and save to. 

Legacy Output Options
=====================

These options are included in v2 for back-compatibility with older versions of trimAl.
New formats will not be added to this list of output format arguments.
The new formats argument "-formats <format1, format2, etc>" should be used instead.

.. option:: -nbrf

Output file in NBRF/PIR format

.. option:: -mega

Output file in MEGA format

.. option:: -nexus

Output file in NEXUS format

.. option:: -clustal

Output file in CLUSTAL format

.. option:: -fasta

Output file in FASTA format

.. option:: -fasta_m10

Output file in FASTA format.
Sequences name length up to 10 characters.

.. option:: -phylip

Output file in PHYLIP/PHYLIP4 format.

.. option:: -phylip_m10

Output file in PHYLIP/PHYLIP4 format.
Sequences name length up to 10 characters.

.. option:: -phylip_paml

Output file in PHYLIP format compatible with PAML.

.. option:: -phylip_paml_m10

Output file in PHYLIP format compatible with PAML.
Sequences name length up to 10 characters.

.. option:: -phylip3.2

Output file in PHYLIP3.2 format.

.. option:: -phylip3.2_m10

Output file in PHYLIP3.2 format.
Sequences name length up to 10 characters.

Report Output
====================
.. option:: -htmlout <outputfile>

Get a summary of trimal's work in an HTML file.

.. option:: -svgout <outputfile>
.. option:: -svgout <outputfile> (v2)

Get a summary of trimal's work in a SVG file.

.. option:: -sgvstats <outputfile>
.. option:: -sgvstats <outputfile> (v2)

Get a summary of trimal's calculated stats in a SVG file.

Expand Down Expand Up @@ -125,10 +189,14 @@ Backtranslation Options

Trimming Parameters
=======================
.. option:: --degenerated_nt_identity
.. option:: --degenerated_nt_identity (v2)

Specify the degenerated nt identity matrix as the similarity matrix to use.

.. option:: --alternative_matrix <name> (v1.4)

Select an alternative similarity matrix already loaded. Only available 'degenerated_nt_identity'.

.. option:: -matrix <inputfile>

Input file for user-defined similarity matrix (default is Blosum62).
Expand All @@ -152,7 +220,8 @@ Trimming Parameters
Get the complementary alignment in residues.
Reverses the effect of residue trimming:
All residues that were to be removed are kept and vice versa.
.. option:: -complementaryseq

.. option:: -complementaryseq (v2)

Get the complementary alignment in sequences.
Reverses the effect of sequence trimming:
Expand Down Expand Up @@ -189,7 +258,7 @@ Manual Trimming - Thresholds
Range: [0 - 1]
Not compatible with -gat.

.. option:: -gat -gapabsolutethreshold <n>
.. option:: -gat -gapabsolutethreshold <n> (v2)

Max number of gaps allowed on a column to keep it.
Range: [0 - (number of sequences - 1)]
Expand Down Expand Up @@ -241,10 +310,6 @@ Overlap Trimming
in order to be conserved.
Range: [0 - 100](see User Guide).


Automated
------------

.. option:: -nogaps

Remove all positions with gaps in the alignment.
Expand All @@ -253,11 +318,14 @@ Automated

Remove columns composed only by gaps.

.. option:: -noduplicateseqs
.. option:: -noduplicateseqs (v2)

Removes sequences that are equal on the alignment.
It will keep the latest sequence in the alignment.

Automated
------------

.. option:: -gappyout

Use automated selection on "gappyout" mode.
Expand Down Expand Up @@ -351,15 +419,15 @@ Statistics to be calculated and outputted by trimAl
Print overlap scores matrix for all sequences in the input alignment.
(see User Guide).

NGS Support - VCF SNP MSA creator
====================================
NGS Support - VCF SNP MSA creator (v2)
======================================
Suport for VCF files. Providing a reference genome,
and one or more VCF, multiple MSA are created.
One MSA for each contig present on the whole VCF-dataset.
Each MSA contains the reference sequence
and a sequence for each donor, with their SNP applied.

.. option:: -vcf <inputfile,...>
.. option:: -vcf <inputfile,...> (v2)

Specify one or more VCF files to produce MSAs
using the input file (-in <n>) as reference genome.
Expand All @@ -379,83 +447,23 @@ and a sequence for each donor, with their SNP applied.
or it doesn't contain the tag "[contig]",
the sequences names will have the name of their contig prepended.

.. option:: -minquality <n>
.. option:: -minquality <n> (v2)

Specify the min quality of a SNP in VCF to apply it.
Only valid in combination with -vcf.

.. option:: -mincoverage <n>
.. option:: -mincoverage <n> (v2)

Specify the min coverage of a SNP in VCF to apply it.
Only valid in combination with -vcf.

.. option:: -ignoreFilter
.. option:: -ignoreFilter (v2)

Ignore vcf-filtered variants in VCF.
Only valid in combination with -vcf.
Still applies min-quality and min-coverage when provided.


Legacy Options
===============

These options are included for back-compatibility with older versions of trimAl.
New formats will not be added to this list of output format arguments.
The new formats argument "-formats <format1, format2, etc>" should be used instead.

.. option:: -nbrf

Output file in NBRF/PIR format

.. option:: -mega

Output file in MEGA format

.. option:: -nexus

Output file in NEXUS format

.. option:: -clustal

Output file in CLUSTAL format

.. option:: -fasta

Output file in FASTA format

.. option:: -fasta_m10

Output file in FASTA format.
Sequences name length up to 10 characters.

.. option:: -phylip

Output file in PHYLIP/PHYLIP4 format.

.. option:: -phylip_m10

Output file in PHYLIP/PHYLIP4 format.
Sequences name length up to 10 characters.

.. option:: -phylip_paml

Output file in PHYLIP format compatible with PAML.

.. option:: -phylip_paml_m10

Output file in PHYLIP format compatible with PAML.
Sequences name length up to 10 characters.

.. option:: -phylip3.2

Output file in PHYLIP3.2 format.

.. option:: -phylip3.2_m10

Output file in PHYLIP3.2 format.
Sequences name length up to 10 characters.


Some Examples
======================

Expand Down
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