PXNJ(1)

💖 PXNJ — like, the manual page, but make it make sense 💖

okay bestie, welcome to pxnj, part of the phyx fam, living in section 1 of your friendly neighbourhood Unix manual. this is the basic neighbour-joining tree maker and she is here to turn your sequences into a tree. no cap. 🌳✨

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✨ NAME ✨

pxnj — basic neighbour-joining tree maker 🫶

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🌸 SYNOPSIS 🌸

pxnj [OPTIONS]...

like. that's it. that's the whole vibe. options go in, tree comes out. 💅

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🦋 DESCRIPTION 🦋

Okay so boom: pxnj is a basic neighbour-joining tree maker. It's giving "simple, does one thing, does it well."

It will happily take fasta, fastq, phylip, and nexus inputs — either straight from a file or piped in from STDIN. Not me being flexible or whatever. 😌

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👑 OPTIONS 👑

• -s, --seqf=FILE — your input sequence file. If you don't hand her one, she'll just read from STDIN instead. 🍓
• -n, --nthreads=INT — how many threads you wanna throw at it. default is 1. multitask, queen. 🔥
• -o, --outf=FILE — the output newick file. If you skip it, output goes to STOUT otherwise. (that's literally what the manpage says, I'm not touching it, that's the lore 💀)
• -h, --help — display this help and exit. classic. ✨
• -V, --version — display version and exit. nosey behaviour but valid. 💜
• -C, --citation — display phyx citation and exit. cite your sources, bestie, it's the law. 📚

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🎀 CITATION 🎀

if you use this and you don't cite it, the vibes will be off. so here it is, word for word:

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>.

put that in your paper. slay. 🌈

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💜 AUTHOR 💜

Written by Joseph F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim). iconic trio, honestly. 👑

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🙈 REPORTING BUGS 🙈

Found a bug? Don't suffer in silence, tell the people:

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

they wanna know. fr fr. 🫶

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⭐ COPYRIGHT ⭐

Copyright © 2015-2021 FePhyFoFum

License GPLv3. periodt. 💅

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and that's the whole page, bestie. this was pxnj version 1.2, dated June 2021 — go make some trees and be the main character of your own phylogeny. bye!! 🌸🦋✨