PXSW(1)

💖 PXSW(1) — the pxsw girlies' guide 💖

okay so bestie, welcome to pxsw, a User Command, and honestly? it's giving main character energy for sequence alignment. sit down, grab a boba, and let's get into it 🧋✨

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🌸 NAME 🌸

pxsw — conduct Smith-Waterman analysis for all seqs in a file 💅

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✨ SYNOPSIS ✨

pxsw [OPTIONS]...

that's it. that's the whole vibe. options go in, slay comes out 🫶

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🦋 DESCRIPTION 🦋

So like, pxsw conducts Smith-Waterman analysis for all the seqs in a file. not some of them. all of them. periodt 💅

It will take fasta, fastq, phylip, and nexus formats — from a file or from STDIN, because it's flexible like that 😌

Output is a list of the scores and distances (and the alignments, if you ask nicely). it's giving "I do it all" fr fr 🔥

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🎀 OPTIONS 🎀

• -s, --seqf=FILE — input sequence file, otherwise it reads from STDIN 💖
• -a, --outalnf=FILE — output sequence file; if you don't give one, it just won't output it, no big deal 🙈
• -t, --seqtype=INT — sequence type, default=DNA (DNA=0, AA=1). pick your fighter ✨
• -m, --matrix=FILE — scoring matrix, default DNA=EDNAFULL, AA=BLOSUM62. the defaults ate, ngl 👑
• -n, --nthreads=INT — number of threads (open mp), default=2. two threads is the minimum slay 🧚
• -v, --verbose — make the output more verbose, and heads up bestie: this turns off parallel 😭
• -o, --outf=FILE — output score/distance file, otherwise STOUT 💜
• -h, --help — display this help and exit 🫶
• -V, --version — display version and exit ⭐
• -C, --citation — display phyx citation and exit 🌈

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📚 CITATION 📚

if you're gonna use this in your work (and you should, it's iconic), cite it properly bestie:

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) — the OG, the blueprint 💅

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🚨 REPORTING BUGS 🚨

Found a bug? not the vibe, but okay, let's fix it:

• Report bugs 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, no cap. now go run some alignments and absolutely ate 💅✨🦋

okay so one last thing — this is pxsw version 1.3.1, from June 2024. luv u, bye 🫶💖