PXTSCALE(1)

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

okay so you just pulled up the manual page for pxtscale, a User Commands girlie living in section 1 of the manual, and honestly? she's niche but she serves. Here's everything she does, no gatekeeping 💖

🎀 NAME 🎀

  • pxtscale — tree rescaling by factor or root height

Like, rescale a tree. By a factor. Or by root height. That's the whole vibe. ✨

🌸 SYNOPSIS 🌸

pxtscale [OPTIONS]...

🦋 DESCRIPTION 🦋

So bestie, pxtscale does tree rescaling — and you get to pick your method: you either hand her a scaling factor or a root height. That's it, that's the menu. 🍓

She'll happily take a newick- or nexus-formatted tree from a file or straight from STDIN (she's not picky, she's flexible 💅).

The output? newick format. Always. Periodt.

✨ OPTIONS ✨

  • -t, --treef=FILE — the input tree file 🫶 if you don't give her one, she reads from STDIN instead
  • -s, --scale=DOUBLE — the edge length scaling factor, like the multiplier of your tree's whole situation
  • -r, --rootheight=DOUBLE — height of root, but heads up: the tree must be ultrametric or this is not gonna go how you want 😭
  • -o, --outf=FILE — the output file 🎀 otherwise she writes to STOUT (yes, that's literally what the page says, iykyk)
  • -h, --help — display this help and exit, the classic "just tell me what to do" button
  • -V, --version — display version and exit, for when you need to know exactly which one you're dealing with 👑
  • -C, --citation — display phyx citation and exit, because citing your tools is main character energy, fr fr

📚 CITATION 📚

If you use this, cite your sources bestie, it's giving academic integrity 🌈:

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. Legend behaviour, honestly. 🫡

🐛 REPORTING BUGS 🐛

Found something broken? not me finding a bug — go tell the devs, they want to know 💀

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

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

Copyright © 2016-2024 FePhyFoFum License GPLv3

and that's the whole page, bestie, you're officially literate in pxtscale now 💜 This was pxtscale 1.3.1, dated June 2024 — go forth and rescale those trees, you absolute icon 🌸🦋✨

📦 where this page comes from