PXRECODE(1)

👑 PXRECODE — the recoding page, bestie edition

okay so welcome to pxrecode (that's section 1 of the User Commands manual, for the record) — she's a little tool that does nucleotide sequence recoding and she's honestly iconic 💅

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✨ NAME ✨

pxrecode — nucleotide sequence recoding 🧬

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✨ SYNOPSIS ✨

pxrecode [OPTIONS]...

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✨ DESCRIPTION ✨

So basically: nucleotide sequence recoding. That's the whole vibe. 🦋

She'll take fasta, fastq, phylip, and nexus formats, and she'll take them from a file or from STDIN. Your choice, no pressure, main character energy either way 💖

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✨ OPTIONS ✨

• -s, --seqf=FILE — the input sequence file. If you don't hand her one, she's reading from STDIN instead. no file? no problem 🫶
• -r, --recode=STRING — a string that tells her which recoding scheme you want. the default is RY ✨

These are the supported recodings, and yes you can use any valid combination of them:

R = A|G
Y = C|T
S = C|G
W = A|T
M = A|C
K = G|T
B = C|G|T
D = A|G|T
H = A|C|T
V = A|C|G

• -o, --outf=FILE — the output sequence file. if you skip it, she writes to STOUT instead 💜
• -h, --help — shows you this help and dips out. respect 🙈
• -V, --version — shows you the version and dips out 🌸
• -C, --citation — shows you the phyx citation and dips out. cite your sources, bestie, it's giving academic integrity 📚✨

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✨ CITATION ✨

If you use this and you're being a good little scientist about it, here's the one to cite — copy it exactly, no paraphrasing 🎀

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 👑 (we love him, we thank him)

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✨ REPORTING BUGS ✨

Found a bug? Do NOT suffer in silence, tell the people 😭

• 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 — go recode something gorgeous 🌈

this has been pxrecode version 1.3.1, brought to you by June 2024 🦋 stay slay, stay sequenced, periodt 💅💖