PXTRT(1)

✨ pxtrt ✨

okay so real quick, this is the manual page for pxtrt from the User Commands crew — she traces a big tree from a taxon list and produces newick, and honestly? she eats every single time. 💅

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🌸 NAME 🌸

pxtrt — trace big tree from taxon list and produce newick

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🦋 SYNOPSIS 🦋

pxtrt [OPTIONS]...

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💖 DESCRIPTION 💖

okay bestie listen up, this one is lowkey iconic. pxtrt will trace a big tree given a taxon list and produce newick. that's the whole vibe. 🌈

and the data? she's flexible fr fr — you can read it from a file or from STDIN. your choice, main character.

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🎀 OPTIONS 🎀

• -t, --treef=FILE — the input tree file, bestie. if you don't hand her one she'll just take it from STDIN instead. no pressure 🫶
• -n, --names=CSL — names separated by commas. and pls pls pls — NO SPACES! (this is not a drill, she will not vibe with spaces) 😭
• -f, --namesf=FILE — names in a file instead, each one on its own line. very organized of you 💅
• -c, --comp — take the complement. so like, she removes any taxa not in the list. inverse behavior, iconic behavior ✨
• -s, --silent — suppress those warnings about missing tips. quiet luxury 🌸
• -o, --outf=FILE — output tree file. if you don't specify one she goes to STOUT otherwise (yes, the manpage really says STOUT, we don't make the rules, we just report them 💀)
• -h, --help — display this help and exit. the classic.
• -V, --version — display version and exit. she'll tell you who she is 👑
• -C, --citation — display the phyx citation and exit. give credit where credit is due, it's giving academic integrity 🎓

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💜 CITATION 💜

if you use this in your work, cite her properly bestie, it's the least you can do:

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) and Joseph W. Brown. absolute legends, no cap 🫡

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🙈 REPORTING BUGS 🙈

found a bug? do NOT suffer in silence, 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 © 2017-2024 FePhyFoFum

License GPLv3 — that's the whole legal vibe, periodt. 💅

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and that's the tea, bestie 🍓 — this was pxtrt version 1.3.1, from June 2024. go trace something beautiful 🌸✨