PXNW(1)

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

💅 PXNW — like, the whole manual but make it cute

okay bestie, welcome to pxnw, a whole little legend from the phyx universe (that's the User Commands crew, section 1, iykyk) ✨ she does Needleman-Wunsch analysis and honestly? she ate.

✨ NAME ✨

pxnw — conduct Needleman-Wunsch analysis for all the seqs in a file 🧬

🌸 SYNOPSIS 🌸

pxnw [OPTIONS]...

that's it. that's the whole vibe. options go brrr 💅

🦋 DESCRIPTION 🦋

So basically: conduct Needleman-Wunsch analysis for all the seqs in a file. Not me being obsessed with a pairwise alignment tool but here we are 😭

She'll take fasta, fastq, phylip, and nexus formats — either from a file or straight from STDIN, no judgment, she's flexible like that 🫶

And the output? A list of the scores and distances — plus the alignments too, if you ask for them. main character energy fr fr 👑

💖 OPTIONS 💖

  • -s, --seqf=FILE — your input sequence file, bestie. If you don't give her one, she reads from STDIN instead ✨
  • -a, --outalnf=FILE — output sequence file. If you don't set this, she just won't output one at all, periodt 🙈
  • -t, --seqtype=INT — sequence type, default is DNA (DNA=0, AA=1) 🧬
  • -m, --matrix=FILE — the scoring matrix. defaults are DNA=EDNAFULL and AA=BLOSUM62 🌈
  • -n, --nthreads=INT — number of threads (open mp), default is 2. parallel go brrr 🔥
  • -v, --verbose — makes the output more verbose. heads up tho: this turns off parallel, no cap 💀
  • -o, --outf=FILE — output score/distance file. otherwise it's STOUT 🍓
  • -h, --help — display this help and exit. she's helpful AND iconic 💅
  • -V, --version — display version and exit 👑
  • -C, --citation — display phyx citation and exit. cite your sources, bestie, it's the law 📚

📚 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.

like. look at that DOI. flawless. slay 🎀

🌟 AUTHOR 🌟

Written by Stephen A. Smith (blackrim) 🫶

😭 REPORTING BUGS 😭

Report bugs to: https://github.com/FePhyFoFum/phyx/issues

phyx home page: https://github.com/FePhyFoFum/phyx

(pls be nice, they're doing their best, and also they made this whole thing for free 💖)

Copyright © 2013-2024 FePhyFoFum License GPLv3

and that's the whole page, bestie!! this was pxnw 1.3.1, dated June 2024, living her best life in section PXNW(1) 💅✨ go align something gorgeous 🦋💜

📦 where this page comes from