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tree_pruning.log
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=> Comparing original_tree with pruned_tree_r2t.
Trees have different numbers of tips: 691 and 667.
Tips in original_tree not in pruned_tree_r2t : Coli_007675, Coli_007697, Coli_007801, Coli_007792, Coli_007800, Coli_003258, Coli_012269, Coli_005719, Coli_006811, Coli_006812, Coli_006814, Coli_011042, Coli_006749, Coli_006750, Coli_007927, Coli_007644, Coli_009275, Coli_006650, Coli_006692, Coli_014546, Coli_003393, Coli_005715, Coli_006539, Coli_019714.
Trees have different numbers of nodes: 689 and 665.
Both trees are unrooted.
Both trees are not ultrametric.
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=hu_HU.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=hu_HU.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=hu_HU.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=hu_HU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] magrittr_2.0.3 lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.1 purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.1 tidyverse_2.0.0 optparse_1.7.3
loaded via a namespace (and not attached):
[1] nlme_3.1-162 bitops_1.0-7 ggtree_3.7.1.003 doParallel_1.0.17 GenomeInfoDb_1.34.9 numDeriv_2016.8-1.1 tools_4.2.1 utf8_1.2.3 R6_2.5.1 lazyeval_0.2.2
[11] BiocGenerics_0.44.0 colorspace_2.1-0 withr_2.5.0 tidyselect_1.2.0 gridExtra_2.3 mnormt_2.1.1 phangorn_2.11.1 compiler_4.2.1 textshaping_0.3.6 cli_3.6.1
[21] expm_0.999-7 labeling_0.4.2 scales_1.2.1 mvtnorm_1.1-3 quadprog_1.5-8 systemfonts_1.0.4 digest_0.6.31 yulab.utils_0.0.6 XVector_0.38.0 pkgconfig_2.0.3
[31] plotrix_3.8-2 maps_3.4.1 rlang_1.1.0 rstudioapi_0.14 optimParallel_1.0-2 gridGraphics_0.5-1 generics_0.1.3 farver_2.1.1 combinat_0.0-8 jsonlite_1.8.4
[41] RCurl_1.98-1.12 ggplotify_0.1.0 GenomeInfoDbData_1.2.9 patchwork_1.1.2 Matrix_1.5-3 Rcpp_1.0.10 munsell_0.5.0 S4Vectors_0.36.2 fansi_1.0.4 ape_5.7-1
[51] viridis_0.6.2 lifecycle_1.0.3 scatterplot3d_0.3-43 stringi_1.7.12 clusterGeneration_1.3.7 MASS_7.3-58.3 zlibbioc_1.44.0 grid_4.2.1 parallel_4.2.1 crayon_1.5.2
[61] lattice_0.20-45 Biostrings_2.66.0 hms_1.1.3 pillar_1.9.0 igraph_1.4.1 caper_1.0.1 codetools_0.2-19 stats4_4.2.1 fastmatch_1.1-3 glue_1.6.2
[71] ggfun_0.0.9 vctrs_0.6.1 treeio_1.23.1 tzdb_0.3.0 foreach_1.5.2 gtable_0.3.3 getopt_1.20.3 phytools_1.5-1 tidytree_0.4.2 coda_0.19-4
[81] ragg_1.2.5 viridisLite_0.4.1 iterators_1.0.14 aplot_0.1.10 IRanges_2.32.0 timechange_0.2.0