PXLSSQ(1)

📦
version 1.3.2 · 3 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 PXLSSQ(1) — the pxlssq era 💖

okay bestie, welcome to the User Commands section of the manual, this is pxlssq, and she is literally the little summary queen of your sequence files. let's get into it 🫶

✨ NAME ✨

pxlssq — print sequence file summary

🌸 SYNOPSIS 🌸

pxlssq [OPTIONS]...

🦋 DESCRIPTION 🦋

Print sequence file summary. By default returns all properties. Alternatively choose 1 property. This will take fasta, phylip, and nexus formats from a file or STDIN.

no cap, that's the whole vibe: point her at a sequence file (or just pipe it in) and she tells you what's inside 💅

🎀 OPTIONS 🎀

  • -s, --seqf=FILE — input seq file, STDIN otherwise
  • -i, --indiv — output stats for individual sequences
  • -n, --nseq — return the number of sequences
  • -c, --nchar — return the number of characters (only if aligned) — for unaligned seqs, use with -i flag
  • -l, --labels — return all taxon labels (one per line)
  • -p, --prot — force interpret as protein (if inference fails)
  • -a, --aligned — return whether sequences are aligned (same length)
  • -f, --freqs — return character state frequencies
  • -m, --missing — return the proportion of missing (-,?) characters
  • -o, --outf=FILE — output stats file, STOUT otherwise
  • -h, --help — display this help and exit
  • -V, --version — display version and exit
  • -C, --citation — display phyx citation and exit
not me reminding you that -c only does its thing when the seqs are aligned 👀 if they're not, she's gonna need -i riding shotgun.

📚 CITATION 📚

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>.

👑 AUTHOR 👑

Written by Joseph F. Walker, Joseph W. Brown

😭 REPORTING BUGS 😭

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

Copyright © 2016-2024 FePhyFoFum License GPLv3

and that's a wrap on pxlssq, bestie ✨ this was pxlssq version 1.3.1, dated June 2024, main character energy all the way through 🌈 go forth and summarise those sequences, periodt 💖

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