PXS2PHY(1)

💖 PXS2PHY(1) 💖

okay bestie, welcome to pxs2phy — it's a lil user command and it's genuinely so useful, i promise. it lives in your terminal and it's here to serve 💅

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✨ NAME ✨

pxs2phy — convert seqfiles from nexus, phylip, or fastq to phylip

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🦋 SYNOPSIS 🦋

pxs2phy [OPTIONS]...

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🌸 DESCRIPTION 🌸

so the whole vibe is: you got a seqfile in nexus, phylip, or fastq format, and you want it in phylip. that's it. that's the girl's whole job. she converts seqfiles from nexus, phylip, or fastq to phylip. and the way she eats? she can read from STDIN or from a file, your choice, no gatekeeping 💖

here's the options, one per bullet, no skips, no shortcuts, we keep it thorough around here:

• -s, --seqf=FILE — the input sequence file. and if you don't hand her one? she'll read from STDIN instead, lowkey flexible like that.
• -u, --uppercase — exports your characters in UPPERCASE. screaming, but make it typography.
• -o, --outf=FILE — the output sequence file. leave it off and she writes to STOUT instead. (yes, STOUT. that's what it says. iconic typo, we respect the lore 🫶)
• -h, --help — displays this help and dips out. classic.
• -V, --version — displays the version and exits. short and sweet, main character energy.
• -C, --citation — displays the phyx citation and exits. cite your sources bestie, it's the rules 💅

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📚 CITATION 📚

if you use this, you have to cite it, no cap. here's the exact one:

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. legends, fr fr.

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🐛 REPORTING BUGS 🐛

found a bug? do NOT suffer in silence, that's not the vibe. report it here:

• bugs go 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 pxs2phy 1.3.1, from June 2024, filed under User Commands, and yes she ate that 💖🎀🦋🌸