BP_PAIRWISE_KAKS(1p)

📦
version 1.7.3 · 3 versions
, in debian bookworm, debian trixie

💖 bp_pairwise_kaks 💖

okay bestie, gather round, because we're about to talk about bp_pairwise_kaks — literally the script that calculates pairwise Ka, Ks for a whole set of sequences. it lives in the User Contributed Perl Documentation section of the manual, and honestly? it's giving evolutionary biology main character energy. 🧬✨

VERSION: this is version 1.7.3, periodt. 💅

🌸 SYNOPSIS 🌸

bp_pairwise_kaks.PLS -i INPUT-cDNA [-f FORMAT] [-o OUTPUT] \
    [--msa tcoffee|clustal] [--kaks yn00|codeml]

🦋 DESCRIPTION 🦋

so here's the tea, bestie. this script takes a whole dataset of cDNA sequences as input, and then it goes off:

  • it verifies that they contain no stop codons (no cap, it checks)
  • it aligns them in protein space 🧚
  • it projects the alignment back into cDNA 🔥
  • and then it estimates the Ka (non-synonymous) and Ks (synonymous) substitutions, based on the Maximum Likelihood method of Yang, using the PAML package 👑

but like, real talk for a sec 🙈 — often there are specific specific parameters you want to run when you're computing Ka/Ks ratios, so please consider this script a starting point and do not rely on it for every situation. it's not your therapist, it's your launching pad. 💖

✨ OPTIONS ✨

  • -i, --input — the input file with the cDNA sequences. it must have at least two sequences, and it has to be in a format that Bio::SeqIO is capable of reading. also, if Bio::SeqIO is unable to automatically identify the format, you gotta specify the -f option. and technically this isn't even an option — it's a required value. like, mandatory. no skipping bestie. 🫶
  • -f, --format — specify the format of INPUT-cDNA for Bio::SeqIO.
  • -o, --output — specify the file for output. defaults to STDOUT, so if you don't say anything it just yells into your terminal. iconic behavior tbh. 📢
  • --msa — program used for alignment, either clustalw or tcoffee. defaults to clustalw.
  • --kaks — program used for the Ka/Ks estimation, either codeml or yn00. defaults to codeml.
  • -v, --verbose — be verbose. be loud. be seen. 💅
  • -h, --help — print help text. it's giving helpful. 🎀

💌 FEEDBACK 💌

📬 Mailing lists

user feedback is an integral part of the evolution of this and other Bioperl modules, fr fr. send your comments and suggestions preferably to the Bioperl mailing list. your participation is much appreciated, bestie, no cap. 🥹

bioperl-l@bioperl.org              - General discussion
http://bioperl.org/Support.html    - About the mailing lists

🫶 Support

please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. many experienced and reponsive experts will be able look at the problem and quickly address it. please include a thorough description of the problem with code and data examples if at all possible. 🔍✨

🐛 Reporting bugs

report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/bio-tools-phylo-paml/issues

👑 AUTHOR 👑

Jason Stajich <jason@bioperl.org>

this software is copyright (c) by Jason Stajich <jason@bioperl.org>.

this software is available under the same terms as the perl 5 programming language system itself.

and that's a wrap, bestie 🎀 this page came to you from <rainbow>perl v5.34.0</rainbow>, dated 2022-10-14, in the good old BP_PAIRWISE_KAKS(1p) manual. slay, go compute some Ka/Ks, and remember: no stop codons. 💖🦋🌸

📦 where this page comes from