PXCAT(1)

💖 PXCAT — sequence file concatenation 💖

okay bestie, welcome to pxcat, part of the phyx crew (User Commands, obvs) — she's the girl who takes all your lil sequence files and smooshes them into ONE. main character energy fr.

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✨ SYNOPSIS ✨

pxcat [OPTIONS]... FILES

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🦋 DESCRIPTION 🦋

Sequence file concatenation. no cap, that's literally the whole job. she can use wildcards too, like:

pxcat -s *.phy -o my_cat_file.fa

but okay so — if your argument list gets too long (the shell has a limit, she's not being dramatic, it's real), you gotta put the filenames in a file instead:

for x in *.phy

do echo $x >> flist.txt

done

and then call her using the -f option:

pxcat -f flist.txt -o my_cat_file.fa

she takes fasta, fastq, phylip, and nexus sequence formats 💅 and here's the iconic part: individual files may be of different formats. mix and match, she doesn't care, she eats. 🔥

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✨ OPTIONS ✨

• -s, --seqf=FILE — list of input sequence files (space delimited)
• -f, --flist=FILE — file listing input files (one per line)
• -p, --partf=FILE — output partition file, none otherwise
• -u, --uppercase — export characters in uppercase
• -o, --outf=FILE — output sequence file, STOUT otherwise
• -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 her in your paper (and you should, she ate), cite her 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 Joseph F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim) — the icons, the legends, the founding mothers (metaphorically). 👑

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🙈 REPORTING BUGS 🙈

found a bug? not the vibe, but okay, tell the devs:

• 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, bestie!! ✨ this was pxcat version 1.3.1, from way back in June 2024 — courtesy of the phyx girls, slay, mwah 💖🦋🎀