PXCLTR(1)

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

💖 PXCLTR — the general tree cleaner 💖

okay bestie, gather round, because this is pxcltr, manual section 1, from the User Commands corner of the universe, and she is iconic. ✨

🌸 NAME 🌸

pxcltr — your general tree cleaner, no cap 🧹🌳

🎀 SYNOPSIS 🎀

pxcltr [OPTIONS]...

✨ DESCRIPTION ✨

So basically, she's a general tree cleaner. 💅 What she does is strip out annotations (those are node labels, btw), the 'knuckles' (which are 2-degree nodes, iykyk), and root edges — all so she can hand you back a fresh, 'vanilla' newick representation. Obsessed.

By default she removes all properties. Or, alternatively, you can choose 1 property. Pick your fighter, bestie.

She'll happily take a newick- or nexus-formatted tree from a file, or straight from STDIN. And the output? Written in newick format. Periodt. 🌈

👑 OPTIONS 👑

  • -t, --treef=FILE — the input treefile, babes. If you don't hand her one, she reads from STDIN instead 🫶
  • -r, --root — remove the root edge (if it's even there, no pressure)
  • -l, --labels — remove internal node labels 🏷️
  • -k, --knuckles — remove those 2-degree internal nodes, bye knuckles 👋
  • -o, --outf=FILE — the output file. Otherwise it's STOUT 💀
  • -h, --help — display this help and exit, your lil cheat sheet 🎀
  • -V, --version — display version and exit ⭐
  • -C, --citation — display phyx citation and exit, because we give credit around here 💜

📚 CITATION 📚

If you're gonna use her in your work (and you should, she ate), cite her properly:

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. main character energy fr fr 💖

🙈 REPORTING BUGS 🙈

Found a bug? Not me being dramatic but tell someone!! 😭

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

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

Copyright © 2017-2024 FePhyFoFum License GPLv3

and that's the whole vibe check bestie 🫶 this was pxcltr version 1.3.1, living her truth since June 2024 🌸💅✨

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