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

       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.

perl v5.36.0                                       2022-10-14                               BP_PAIRWISE_KAKS(1p)

       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.

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       data examples if at all possible.

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

-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.

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

       version 1.7.3