PXMRCACUT(1)

💖 PXMRCACUT 💖

okay bestie, welcome to pxmrcacut, section 1 of the User Commands girlies ✨ this one's the phyx tool that goes snip snip on your trees 🦋

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🌸 NAME 🌸

pxmrcacut — extract subclades from trees 🎀

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✨ SYNOPSIS ✨

pxmrcacut [OPTIONS]...

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🧚 DESCRIPTION 🧚

So the whole vibe is: extract subclade(s) from tree(s). no cap, that's literally it 💅

Here's the tea: it takes a newick- or nexus-formatted tree, either from a file or from STDIN 🫶. And then you hand it an MRCA file, which has this format:

MRCANAME = tip1 tip2 ...

and if you give it multiple MRCAs, you get multiple subtrees back. iconic behavior honestly 👑

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🎀 OPTIONS 🎀

• -t, --treef=FILE — the input newick tree file 🗂️ … and if you don't give one? STDIN it is, bestie.
• -m, --mrca=FILE — the file holding your MRCA declarations 💖
• -o, --outf=FILE — the output newick file, or STOUT otherwise 🌈
• -h, --help — show this help and dip ✌️
• -V, --version — show the version and dip ✌️
• -C, --citation — show the phyx citation and dip ✌️

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📚 CITATION 📚

if you're gonna use this in your work, pls pls pls cite the girlies 🙏:

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 Stephen A. Smith (blackrim), Joseph W. Brown 💜 absolute legends fr fr

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🐛 REPORTING BUGS 🐛

found a bug? 😭 don't suffer in silence, report it to: <https://github.com/FePhyFoFum/phyx/issues>

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

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⭐ COPYRIGHT ⭐

Copyright © 2013-2024 FePhyFoFum License GPLv3 📜

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and that's the whole page bestie 💅 pxmrcacut 1.3.1, dated June 2024 — go forth and cut some clades, you got this 🦋💖🎀