PXTCOL(1)

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

🎀 PXTCOL 💅

okay bestie, so pxtcol is a lil Unix user command, section 1, and it's about to make your phylogenies ✨aesthetic✨

✨ NAME ✨

pxtcol — add information to color edges of a tree 🎨🌳

🌸 SYNOPSIS 🌸

pxtcol [OPTIONS]...

🦋 DESCRIPTION 🦋

So here's the vibe: pxtcol adds information to a tree so that you can color the edges. Like, you're literally decorating your tree, and honestly? It ate. 💖

It takes nexus and newick inputs from a file or from STDIN. No cap.

Then the results get written in nexus format so that it can be read by figtree. Yes bestie, we're making it figtree-compatible, because we're considerate like that. 🫶

💅 OPTIONS 💅

  • -t, --treef=FILE — input tree file, STDIN otherwise 🌳 (if you don't hand it a file, it's gonna read from standard input, iykyk)
  • -m, --mrcaf=FILE — file with mrcas and annotations, tab separated 📋 (tab separated, fr fr, don't use spaces)
  • -d, --nodeidf=FILE — file with nodeids (labels) and annotations, tab separated 🏷️ (also tab separated, we're consistent here)
  • -o, --outf=FILE — output file, STOUT otherwise 📤
  • -h, --help — display this help and exit 🙋‍♀️ (she's helpful like that)
  • -V, --version — display version and exit 👑
  • -C, --citation — display phyx citation and exit 📚 (academic bestie behavior, we love to see it)

🌈 CITATION 🌈

if you use this in your paper (and you should, it's iconic), cite the girls:

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) — king behavior, honestly 💜

🙈 REPORTING BUGS 🙈

found a bug? not the vibe. Report bugs to: <https://github.com/FePhyFoFum/phyx/issues> phyx home page: <https://github.com/FePhyFoFum/phyx>

Copyright © 2016-2024 FePhyFoFum License GPLv3

lowkey important: this is pxtcol version 1.3.1, and this whole page is dated June 2024 🗓️✨

k byeee, go color those edges bestie, you're gonna slay 🌸🦋💖

📦 where this page comes from