PXMRCANAME(1)

💖 PXMRCANAME 💖

okay bestie, welcome to pxmrcaname — a lil User Command that labels internal nodes with clade names ✨ it's giving tree-glowup energy and honestly? obsessed. 🎀

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✨ NAME ✨

pxmrcaname — label internal nodes with clade names 🏷️🌳

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🌸 SYNOPSIS 🌸

pxmrcaname [OPTIONS]...

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🦋 DESCRIPTION 🦋

So the whole vibe here is: you got a tree, and you want to label internal nodes with clade names. That's it, that's the job. 👑

It'll take a newick- or nexus-formatted tree from a file or from STDIN, plus an MRCA file that looks like this:

MRCANAME = tip1 tip2 ...

no cap, that's the format. 🍓

If there's no MRCA file present, the internal nodes just get labelled:

px1, px2, ..., pxn

which is fine, it's giving placeholder realness 💅

Output is written in newick format. periodt.

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🌈 OPTIONS 🌈

• -t, --treef=FILE — input newick tree file; if you don't hand one over, it reads from STDIN instead 🫶
• -m, --mrca=FILE — file containing MRCA declarations 📄✨
• -o, --outf=FILE — output newick file; otherwise it goes to STOUT 💾 (yes, STOUT, that's what it says, we don't question the king 😭)
• -h, --help — display this help and exit, the classic escape hatch 🙈
• -V, --version — display version and exit ⭐
• -C, --citation — display phyx citation and exit 👑

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📚 CITATION 📚

if you're gonna cite this icon, cite it right:

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 🧚

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😭 REPORTING BUGS 😭

found a bug? don't be shy, 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 💖 this was pxmrcaname 1.3.1, born June 2024, brought to you by the FePhyFoFum girlies — slay, stay labeled, and may all your internal nodes know their names 🌸🦋✨