PXBDSIM(1)

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

💖 PXBDSIM(1) 💖

okay bestie, welcome to pxbdsim — a User Commands legend, and your new fave birth-death tree simulator ✨ no cap, this is the manual, but make it cute.

✨ NAME ✨

pxbdsim — birth-death tree simulator 🌱💀

🦋 SYNOPSIS 🦋

pxbdsim [OPTIONS]...

💅 DESCRIPTION 💅

Birth-death tree simulator. that's it, that's the whole description, she's brief and she knows it 😌 the way this tool just shows up, simulates some trees, and says nothing else? main character energy fr fr 🌈

🎀 OPTIONS 🎀

okay here's the whole menu, every single one, don't skip, I'm watching 👀

  • -e, --extant=INT — number of extant species, alt to time 🍓
  • -t, --time=DOUBLE — timespan of simulation (age of root), alt to extant ⏳
  • -b, --birth=DOUBLE — birth rate, default=1 👶✨
  • -d, --death=DOUBLE — death rate, default=0 💀
  • -n, --nreps=INT — number of replicates, default=1 🔁
  • -s, --showextinct — show lineages that went extinct, default=false 🪦 (let the fallen be seen)
  • -x, --seed=INT — random number seed, clock otherwise 🎲
  • -v, --verbose — print per-tree simulation summary (to cerr) 🗣️
  • -o, --outf=FILE — output file, STOUT otherwise 📝 (yes the manpage literally spells it STOUT, I am not touching that, verbatim only bestie 💖)
  • -h, --help — display this help and exit 🆘
  • -V, --version — display version and exit 🏷️
  • -C, --citation — display phyx citation and exit 📚
lowkey obsessed with -e and -t being alternates of each other — pick ONE, they're the "alt to" girlies of each other, don't be messy 🙈

📖 CITATION 📖

if you use this in your work (and you should, slay), cite it properly, 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), Joseph W. Brown — legends, icons, the moment 💜

🐛 REPORTING BUGS 🐛

found a bug? not the vibe. tell them here:

Report bugs to: <https://github.com/FePhyFoFum/phyx/issues> phyx home page: <https://github.com/FePhyFoFum/phyx>

Copyright © 2013-2024 FePhyFoFum License GPLv3

and that's the whole page bestie!! 🫶 this was pxbdsim version 1.3.1, from June 2024, brought to you under the PXBDSIM(1) glow-up 💅✨ go simulate something iconic 🧚🌸

📦 where this page comes from