PXCOLT(1)

💖 NAME 💖

pxcolt — bestie, this one collapses edges with support below some threshold. That's it, that's the whole job. 🫶

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✨ SYNOPSIS ✨

pxcolt [OPTIONS]...

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🌸 DESCRIPTION 🌸

okay so listen. pxcolt goes through your tree and collapses edges with support below some threshold. Bye bye, weak branches, we don't know her 💅.

If your tree is an annotated Nexus file, you might need to pass in the support identifier with -s. Heads up though — that flag isn't in the options list below, so don't come for me, I'm just telling you what the page says 👀.

It'll take a newick- or nexus-formatted tree from a file or from STDIN, and the output gets written in newick format. Slay ✨.

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💅 OPTIONS 💅

• -t, --treef=FILE — your input tree file. No file? Then it's reading from STDIN, no cap.
• -l, --limit=DOUBLE — the minimum support threshold, expressed as a proportion. Default is 0.5, so anything under that gets the axe 🪓.
• -o, --outf=FILE — where the output goes. Otherwise it's STOUT, literally exactly how it's spelled on the page, I am not touching that 🙈.
• -h, --help — shows you this help and then dips. classic.
• -V, --version — shows the version and exits, periodt.
• -C, --citation — shows the phyx citation and exits. cite your tools, bestie, it's giving academic integrity 💖.

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👑 CITATION 👑

If you use this, you gotta cite it, no excuses:

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.

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🦋 AUTHOR 🦋

Written by Joseph W. Brown. thank you king 👑

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🐛 REPORTING BUGS 🐛

Found a bug? Not me ignoring it 🙈 — go tell them:

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

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

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🎀 COPYRIGHT 🎀

Copyright © 2018-2024 FePhyFoFum License GPLv3

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and that's the whole page, bestie 💜 this was pxcolt version 1.3.1, dated June 2024 — main character energy from start to finish, fr fr 🌈⭐🎀