Provided by: libbio-tools-phylo-paml-perl_1.7.3-2_all
bp_pairwise_kaks - calculate pairwise Ka,Ks for a set of sequences
bp_pairwise_kaks.PLS -i INPUT-cDNA [-f FORMAT] [-o OUTPUT] \ [--msa tcoffee|clustal] [--kaks yn00|codeml]
This script will take as input a dataset of cDNA sequences, verify that they contain no stop codons, align them in protein space, project the alignment back into cDNA, and estimate the Ka (non-synonymous) and Ks (synonymous) substitutions based on the Maximum Likelihood method of Yang with the PAML package. Often there are specific specific parameters you want to run when you are computing Ka/Ks ratios so consider this script a starting point and do not rely it on for every situation.
-i, --input The input file with the cDNA sequences. Must have at least two sequences, and be in a format that Bio::SeqIO is capable to read. In addition, if Bio::SeqIO is inable to automatically identify the format, the -f option should be specified. Technically not an option, this is a required value. -f, --format Specify the format of INPUT-cDNA for Bio::SeqIO. -o, --output Specify the file for output. Defaults to STDOUT. --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. -h, --help Print help text.
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Jason Stajich <email@example.com>
This software is copyright (c) by Jason Stajich <firstname.lastname@example.org>. This software is available under the same terms as the perl 5 programming language system itself.