PXRMT(1)

📦
version 1.3.2 · 3 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 NAME 💖

pxrmt — remove tree tips by label ✂️🌳

okay so bestie, real talk: you got a phylogenetic tree and some tips you simply do not want anymore? pxrmt is the girl for the job. she's giving "block and delete" energy but for taxa.

✨ SYNOPSIS ✨

pxrmt [OPTIONS]...

🦋 DESCRIPTION 🦋

Remove tree tips by label. periodt. 🎀

She'll take a newick- or nexus-formatted tree from a file or from STDIN, do her little removal ritual, and then hand you back a tree written in newick format. That's it, that's the whole vibe. no cap. 💅

🌸 OPTIONS 🌸

  • -t, --treef=FILE — the input tree file. if you don't give her one she'll just read from STDIN like the flexible queen she is 🫶
  • -n, --names=CSL — names separated by commas. NO SPACES! like fr fr, none, not even one, the commas are doing all the separating here 😭
  • -f, --namesf=FILE — names live in a file instead, each one chilling on its own line 📄
  • -r, --regex=STRING — match tip labels by a regular expression. regex girlies rise 🧚
  • -c, --comp — take the complement, i.e. remove any taxa not in the list. it's giving reverse uno card 🔄
  • -s, --silent — suppress warnings of missing tips. shhh. 🤫 no more "bestie that tip doesn't exist" spam
  • -o, --outf=FILE — output tree file. otherwise it's STOUT 💀 (yes that's what it says, we simply report the lore)
  • -h, --help — display this help and exit. the classic "help me help you" ✨
  • -V, --version — display version and exit 🏷️
  • -C, --citation — display phyx citation and exit. cite your sources bestie, it's the law 📚👑

👑 CITATION 👑

Brown, Joseph W., Joseph F. Walker, and Stephen A. Smith. 2017. Phyx: phylogenetic tools for unix. Bioinformatics 33(12): 1886-1888. https://doi.org/10.1093/bioinformatics/btx063.

if you use this, cite it. main character behavior, honestly 💜

🌈 AUTHOR 🌈

Written by Joseph W. Brown, Stephen A. Smith (blackrim) 🫡 iconic honestly

💀 REPORTING BUGS 💀

Report bugs to: <https://github.com/FePhyFoFum/phyx/issues> phyx home page: <https://github.com/FePhyFoFum/phyx>

found a bug? don't suffer in silence, go tell the group chat 🐛

Copyright © 2014-2024 FePhyFoFum License GPLv3

okay that's the whole page bestie, go forth and prune 🌳✂️✨

this was pxrmt version 1.3.1, from June 2024 — stay slaying 💅💖

📦 where this page comes from