PXAA2CDN(1)

💖 PXAA2CDN — the manual page, bestie edition 💖

okay so welcome to the pxaa2cdn manual page (that's the section 1 of the User Commands manual, iykyk) 🦋 she's a lil command-line girlie from the phyx family and she is SO good at what she does.

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✨ NAME ✨

pxaa2cdn — generate codon alignment from aligned amino acids and unaligned nucleotides 💅

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🌸 SYNOPSIS 🌸

pxaa2cdn [OPTIONS]...

that's it. that's the whole vibe. options only, no positional args, periodt ✨

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🧚 DESCRIPTION 🧚

okay so here's the tea 🍓: pxaa2cdn generates a codon alignment from aligned amino acids and unaligned nucleotides. the amino acids come in already aligned (like, they did the work), and the nucleotides are just raw unaligned babies, and this tool is the matchmaker that brings them together. it's giving wingman energy, fr fr.

important note tho, bestie: taxa that show up in only 1 input file will be removed. if a taxon is only in the AA file and not the nuc file (or vice versa), she's gone. no cap. gotta be in both or you're not invited to the party 🙈

and the inputs? she takes fasta, fastq, phylip, and nexus. so basically all the formats. she's flexible like that 💅

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💅 OPTIONS 💅

• -a, --aaseqf=FILE — the input sequence file for the amino acids. if you don't give her one, she reads from STDIN instead 🫶
• -n, --nucseqf=FILE — the input sequence file for the nucleotides. same deal: no file means STDIN 🌸
• -r, --rmlastcdn — removes the last codon from all nuc sequences. and yes bestie, it means ALL of them, the italics-and-asterisks in the original are literally screaming that at us. default: false 💀
• -s, --stopremove — removes the stop codon from nuc sequences if one is present. only if it's there tho, she's not gonna invent one. default: false 🎀
• -o, --outf=FILE — output fasta file. if you don't specify one, output goes to STOUT otherwise (that's what the page says, character for character, so I'm passing it along untouched, don't @ me 😭)
• -h, --help — displays this help and exits. the classic. the icon. the moment of "wait what were the flags again" 👑
• -V, --version — displays the version and exits ⭐
• -C, --citation — displays the phyx citation and exits. cite your tools, bestie, it's free and it slays 📚✨

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🌈 CITATION 🌈

if you use this, please cite the phyx paper, it's the polite thing to do and honestly it's just good karma:

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 F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim). legends, honestly 🫶

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🐛 REPORTING BUGS 🐛

found a bug? tell the devs, don't suffer in silence bestie:

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

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💜 COPYRIGHT 💜

Copyright © 2015-2024 FePhyFoFum License GPLv3

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and that's the whole page!! go make some codon alignments, you've got this 💖✨🦋🌸🎀

signing off with the deets: this is pxaa2cdn version 1.3.1, dated June 2024, and it lives in the PXAA2CDN(1) manual. slay 💅