PXT2NEX(1)

✨ NAME ✨

okay bestie, say hi to pxt2nex — it's the lil icon that converts from tree file to vanilla Nexus format 💅 (and yes, it lives in section 1 of the manual, aka User Commands, so you already know it's a command-line girlie)

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🌸 SYNOPSIS 🌸

pxt2nex [OPTIONS]...

that's it. that's the whole vibe. options only, no positional drama 🎀

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🦋 DESCRIPTION 🦋

so here's the tea: pxt2nex will convert a tree file to vanilla Nexus format. periodt ✨

it takes a newick- or nexus-formatted tree from a file or from STDIN, and hands you back the goods. that's the whole job and it does it flawlessly, no cap 🫶

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💖 OPTIONS 💖

• -t, --treef=FILE — the input tree file, bestie 🌳. if you don't give it one, it reads from STDIN instead.
• -o, --outf=FILE — where the output tree file goes 💾. if you skip it, output goes to STOUT otherwise.
• -h, --help — shows you this help and then dips. iconic behaviour honestly 👑
• -V, --version — prints the version and exits, quick lil flex ⭐
• -C, --citation — displays the phyx citation and exits 📜 (yes, cite your tools, it's the bare minimum and it's giving respectful)

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🧚 CITATION 🧚

if you use this, you gotta cite it, fr fr:

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, Stephen A. Smith (blackrim) 💜

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💀 REPORTING BUGS 💀

found a bug? not me ignoring it 🙈 go tell the devs:

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

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

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🍓 COPYRIGHT 🍓

Copyright © 2021-2024 FePhyFoFum License GPLv3

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okay that's the whole page, mwah 💋 this was pxt2nex version 1.3.1, dated June 2024 — go convert some trees, you've got this 🫶✨