Provided by: libbio-tools-phylo-paml-perl_1.7.3-3_all bug


       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.


       -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.

           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.

       -v, --verbose
           Be verbose.

       -h, --help
           Print help text.


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       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