PXRLT(1)

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

💅 PXRLT(1) — User Commands

okay bestie, welcome to pxrlt, a whole manual page, and yes it's giving "I know exactly what I'm doing" energy ✨

🦋 NAME

pxrlt — taxon relabelling for trees 🌳✨

🌸 SYNOPSIS

pxrlt [OPTIONS]...

💖 DESCRIPTION

Taxon relabelling for trees. That's the whole vibe, fr fr.

so here's the deal, bestie: you gotta give it two ordered lists of taxa — -c for the current names and -n for the new names. That's one way. OR, if you're feeling regex-y, you can hand it a regex pattern (-p) plus the replacement text (-r) instead. Either path slaps. 💅

It'll take a newick- or nexus-formatted tree from a file or from STDIN, and it writes the output out in newick format. periodt. 🌈

✨ OPTIONS ✨

  • -t, --treef=FILE — the input tree file. no file? it'll read from STDIN instead, no biggie 🎀
  • -c, --cnames=FILE — the file with your current taxon labels in it, one per line 📝
  • -n, --nnames=FILE — the file with your new taxon labels in it, one per line 🦋
  • -p, --pattern=STRING — the regex pattern you wanna replace 🔍
  • -r, --replace=STRING — the replacement pattern 🔁
  • -v, --verbose — makes the output more verbose. say more, queen 🗣️
  • -o, --outf=FILE — the output file, STOUT otherwise 👑
  • -h, --help — display this help and exit. iconic behaviour tbh 🫶
  • -V, --version — display version and exit ⭐
  • -C, --citation — display phyx citation and exit 📚

🎀 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.

👑 AUTHOR

Written by Joseph W. Brown, Stephen A. Smith (blackrim) — absolute legends, no cap 💜

🙈 REPORTING BUGS

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

phyx home page: <https://github.com/FePhyFoFum/phyx>

found a bug? tell the devs, don't suffer in silence bestie 😭 they wanna know fr fr

Copyright © 2018-2024 FePhyFoFum License GPLv3

and that's the whole page!! this was pxrlt version 1.3.1, dated June 2024, from the PXRLT(1) manual — mwah, slay, go relabel some taxa 💖✨🌸

📦 where this page comes from