PXCOMP(1)

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

💖 PXCOMP(1) — the glow-up edition 💖

okay so real quick: this is the manual page for pxcomp, section 1 (User Commands), and bestie, it's giving compositional homogeneity test and it ate. pull up a chair 🎀

✨ NAME ✨

pxcomp — sequence compositional homogeneity test

like. that's the whole vibe. it tests your sequences for compositional homogeneity. no cap. 👑

🌸 SYNOPSIS 🌸

pxcomp [OPTIONS]...

that's it. that's the whole incantation. options go in, magic comes out. ✨

🦋 DESCRIPTION 🦋

so what is this thing actually doing? Sequence compositional homogeneity test. 💅

it runs a Chi-square test for equivalent character state counts across lineages. so like, it's checking whether all your lineages are pulling up with roughly the same character state counts, or whether somebody's out here with a wildly different vibe. if the counts are all over the place, that's a compositional homogeneity problem and pxcomp will clock it. 😭

and it's not picky about format, she's flexible:

  • it will take fasta, phylip, and nexus formats
  • from a file or from STDIN

so you can pipe it, you can point it at a file, whatever's easiest. main character energy either way. 🫶

💅 OPTIONS 💅

here's the whole roster, bestie, no skips, every single one:

  • -s, --seqf=FILE — input seq file. if you don't give her one, she reads from STDIN instead. 🌈
  • -o, --outf=FILE — output stats file. if you don't give her one, she writes to STOUT instead. 🍓
  • -h, --help — display this help and exit. your girl is helpful like that. ✨
  • -V, --version — display version and exit. she knows exactly who she is. 👑
  • -C, --citation — display phyx citation and exit. cite your sources, periodt. 📚
and yes bestie, STOUT is literally what it says in the original — we do not edit the ancestors, we only stan them. 🙈

🎀 CITATION 🎀

if you use this in your work (and you should, she's iconic), cite it like this, exactly:

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. king behavior, honestly. 👑

🧚 REPORTING BUGS 🧚

found a bug? don't suffer in silence, tell the devs:

they wanna know. fr fr. 🫶

Copyright © 2016-2024 FePhyFoFum License GPLv3

that's the license, respect it, it's what keeps the whole ecosystem cute and open. 💖

and that's the page!! this was pxcomp version 1.3.1, dated June 2024. go run your homogeneity test bestie, you're gonna slay 💅✨🦋

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