PXSTREC(1)

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

💖 PXSTREC(1) 💖

okay so bestie, welcome to the pxstrec page — it lives in the User Commands section of the manual and it's literally your girl for state reconstruction. iykyk 🦋

✨ NAME ✨

pxstrec — conduct state reconstruction analyses

like. that's the whole job. state reconstruction. analyses. she does it. 👑

🌸 SYNOPSIS 🌸

pxstrec [OPTIONS]... FILES

options first, files after. that's the order, don't fight it. 💅

🎀 DESCRIPTION 🎀

This will conduct state reconstruction analyses. that's it, that's the description, she's a woman of few words but MANY flags. no cap. 💀

✨ OPTIONS ✨

okay here's the part you actually came for, the flag buffet. all of them. every single one. obsessed. 🍓

  • -d, --dataf=FILE — input data file
  • -w, --datawide — data is in wide format so (001 instead of 2)
  • -z, --dataz — data is in probability format (0,1,0,0)
  • -t, --treef=FILE — input tree file
  • -c, --conf=FILE — configuration file
  • -n, --outstnum=FILE — output file for stochastic mapping number
  • -a, --outstnumany=FILE — output file for stochastic mapping number any
  • -m, --outsttim=FILE — output file for stochastic mapping duration
  • -p, --periods=NUMS — comma separated times
  • -l, --logf=FILE — log file, STOUT otherwise
  • -o, --outanc=FILE — output file for ancestral calc
  • -s, --silent — less verbose output (default: false)
  • -h, --help — display this help and exit
  • -V, --version — display version and exit
  • -C, --citation — display phyx citation and exit
lowkey note that --silent defaults to false, so she's chatty by default. that's just her personality bestie 🫶

📚 CITATION 📚

if you use this in your paper (and you SHOULD, main character energy), cite it, periodt:

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 fr fr 👑

🐛 REPORTING BUGS 🐛

found a bug? not me finding bugs 🙈 tell the people:

Copyright © 2017-2024 FePhyFoFum License GPLv3

and that's the whole vibe check bestie — pxstrec version 1.3.1, dated June 2024, dropping straight from the PXSTREC(1) manual. go reconstruct some states, slay, and hydrate. 💖✨🎀

📦 where this page comes from