PXCLSQ(1)

✨ pxclsq — the manual page but make it a group chat ✨

okay bestie, welcome to pxclsq from the User Commands corner of the manual. it's a phyx tool, it's 1.3.1, and it's here to clean up your alignments when they're being messy with ambiguous data. let's go 💅

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🌸 NAME 🌸

pxclsq — clean positions or taxa with too much ambiguous data 🧚

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🎀 SYNOPSIS 🎀

pxclsq [OPTIONS]...

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🦋 DESCRIPTION 🦋

so the whole vibe here is: you've got an alignment, and some of it is just noise — positions or taxa that are drowning in ambiguous data. pxclsq cleans that up for you. ✨

it'll happily eat fasta, fastq, phylip, and nexus formats, either from a file or straight from STDIN (yes she takes piped input, queen behavior). and the results come out as fasta format. periodt. 💖

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💅 OPTIONS 💅

• -s, --seqf=FILE — your input sequence file. if you don't give one, she reads from STDIN instead 🫶
• -p, --prop=DOUBLE — the proportion that's required to be present. default is 0.5 ⭐
• -e, --empty — yeets any columns that are completely empty, like literally all - or all ? 💀
• -m, --min=INT — the minimum number of good characters required per site. and ngl, a min of 1 is exactly equivalent to -e up above 👑
• -t, --taxa — flip it to consider missing data per taxon instead of per site (default is per site) 🌈
• -c, --codon — examine sequences by codon instead of by site. heads up though: this requires that all sequences be in frame and of correct length ⚠️
• -i, --info — report counts of missing data and then exit. combine with -t to get the report by taxon (rather than by site), and combine with -c to use codons as the units 📊
• -v, --verbose — more verbose output, like for example if entire seqs get removed 👀
• -o, --outf=FILE — your output fasta file. otherwise it goes to STOUT 🌸
• -h, --help — display this help and exit ✨
• -V, --version — display version and exit 🎀
• -C, --citation — display the phyx citation and exit 📜

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📜 CITATION 📜

if you use this in your research, cite the girlies:

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) 🫶

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🐛 REPORTING BUGS 🐛

found a bug? don't suffer in silence bestie, report it:

• bugs: <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, no cap. this was pxclsq version 1.3.1, dated June 2024, and honestly? she ate. go clean those alignments, bestie 🦋✨💅