PXBP(1)

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

💖 PXBP(1) — bestie edition 💖

okay so. the manual name is pxbp and this whole thing lives in the User Commands section, one command, and it's genuinely so useful. buckle up 🎀

✨ NAME ✨

pxbp — print out bipartitions found in treefiles. that's it. that's the job. 💅

🌸 SYNOPSIS 🌸

pxbp [OPTIONS]...

🦋 DESCRIPTION 🦋

okay so what this does: it prints out the bipartitions it finds in a treefile. 🌈

here's the vibe check you need to know though: trees are assumed to be rooted unless you hand it the -e argument. so if you're sitting there like "why is this treating my tree as rooted," that's why bestie 😭

and it'll happily take a newick- or nexus-formatted tree, either from a file or straight from STDIN. very flexible, we love that for us 🫶

✨ OPTIONS ✨

  • -t, --treef=FILE — the input treefile. if you don't give one, it reads from STDIN instead 🌸
  • -v, --verbose — give more output. more words, more lore, more everything ✨
  • -e, --edgeall — force edgewise (not node — so like, when things are unrooted) and assume all taxa are present in all trees 👑
  • -u, --uniquetree — output unique trees and no other output. nothing else. just the trees. periodt 💅
  • -m, --maptree=FILE — puts the bipart freq on the edges of this tree. this will create a *.pxbpmapped.tre file 📝
  • -c, --cutoff — skip biparts that have support lower than this ✂️
  • -s, --suppress — don't print all the output (maybe you use this with the maptree feature 👀)
  • -o, --outf=FILE — output file, STOUT otherwise (yes bestie, STOUT. that's literally what it says, i don't make the rules 💀)
  • -h, --help — display this help and exit 🫶
  • -V, --version — display version and exit ⭐
  • -C, --citation — display phyx citation and exit 📚

💜 CITATION 💜

if you use this, cite it, because credit is cute:

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) 👑

🙈 REPORTING BUGS 🙈

found a bug? not me ignoring it bestie, go tell them:

Copyright © 2017-2024 FePhyFoFum License GPLv3

and that's the whole page bestie, you ate 💖 this was pxbp 1.3.1 from June 2024 — go print some bipartitions, ily, mwah 🫶💅✨

📦 where this page comes from