PXPOLY(1)

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

✨ PXPOLY ✨

okay so bestie, gather round 💖 this is pxpoly, a lil User Command (section 1 of the manual, iykyk) that takes your polytomies and just... breaks them up into a full binary tree. randomly. it's giving glow-up for your phylogeny 🌸

🦋 NAME 🦋

pxpoly — randomly sample polytomies to generate a binary tree 💅

🎀 SYNOPSIS 🎀

pxpoly [OPTIONS]...

✨ DESCRIPTION ✨

So here's the tea ☕ — pxpoly randomly samples polytomies to generate a binary tree. It's literally just vibing and picking resolutions for you.

⚠️ lowkey important: currently only works with rooted trees (and yes, it does check, so don't try it 🙈). Output is written in newick format.

💅 OPTIONS 💅

  • -t, --treef=FILE — the input tree file, bestie. if you don't hand one over, it reads from STDIN instead 🫶
  • -x, --seed=INT — random number seed. want your randomness to be reproducible? drop an INT here. don't? it'll just use the clock instead ⏰
  • -o, --outf=FILE — output file. no file? it goes to STOUT otherwise 💀 (yes, that's what it says, character for character, no notes)
  • -h, --help — display this help and exit. iconic behaviour honestly 👑
  • -V, --version — display version and exit 🌈
  • -C, --citation — display the phyx citation and exit. cite your sources, it's the rules 📚

🧚 CITATION 🧚

If you use this, you GOTTA cite it, no cap:

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 🫶

😭 REPORTING BUGS 😭

Found a bug? not me being personally victimised 💀 report bugs to: <https://github.com/FePhyFoFum/phyx/issues>

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

Copyright © 2021-2024 FePhyFoFum

License GPLv3 — slay, and also legally binding, so respect it fr fr ⭐

and that's the whole page, bestie!! this was pxpoly version 1.3.1, living its best life back in June 2024 💖 mwah, go binary-ify some polytomies 🦋✨

📦 where this page comes from