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BP_PAIRWISE_KAKS(1p) User Contributed Perl Documentation BP_PAIRWISE_KAKS(1p)


bp_pairwise_kaks - calculate pairwise Ka,Ks for a set of sequences


version 1.7.3


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.


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.

Specify the format of INPUT-cDNA for Bio::SeqIO.
Specify the file for output. Defaults to STDOUT.
Program used for alignment, either clustalw or tcoffee. Defaults to clustalw.
Program used for the Ka/Ks estimation, either codeml or yn00. Defaults to codeml.
Be verbose.
Print help text.


Mailing lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.              - General discussion    - About the mailing lists


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

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:


Jason Stajich <>


This software is copyright (c) by Jason Stajich <>.

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

2022-10-14 perl v5.34.0