PXRR(1)

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

✨ pxrr — like, the tree rerooter 💅

okay bestie, welcome to the pxrr manual page (that's section 1 of the User Commands, iykyk) 🎀

🌸 NAME 🌸

pxrr — reroot (or unroot) a tree file and produce a newick ✨

🦋 SYNOPSIS 🦋

pxrr [OPTIONS]...

💖 DESCRIPTION 💖

okay so here's the whole vibe: pxrr will reroot (or unroot) a tree file and produce a newick. that's the job. that's the whole thing. 👑

it takes a newick- or nexus-formatted tree from a file or from STDIN. and then the output? written in newick format. periodt. 💅

🎀 OPTIONS 🎀

  • -t, --treef=FILE — the input tree file, bestie. if you don't hand one over it'll just read STDIN instead 🫶
  • -g, --outgroups=CSL — your outgroups, separated by commas. NO SPACES! like literally not even one, she WILL notice 😭
  • -f, --namesf=FILE — outgroups in a file instead, each one chilling on its own line 🌸
  • -r, --ranked — turn on ordering of outgroups. it'll root on the first one present 👑
  • -u, --unroot — unroot the tree 🙈
  • -s, --silent — do not error if outgroup(s) not found. she's being chill about it, no drama 💀
  • -o, --outf=FILE — output tree file. otherwise it's STOUT for you (yes, that's exactly what the page says, we don't fix it, we respect it 💜)
  • -h, --help — display this help and exit, iconic behaviour ⭐
  • -V, --version — display version and exit 💅
  • -C, --citation — display phyx citation and exit, academic queen behaviour 🎓✨

📚 CITATION 📚

if you use this, cite her, she deserves it 🥹:

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

🐛 REPORTING BUGS 🐛

found a bug? not the vibe, tell them here:

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

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

Copyright © 2014-2024 FePhyFoFum

License GPLv3

okay that's the whole page, you're literally a pxrr expert now 🌈✨ this was pxrr version 1.3.1, from June 2024, and yeah she's page PXRR(1) in the User Commands section. slay, go root some trees, ily bye 🎀💖🦋

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