NAME

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

VERSION

       version 1.7.3

SYNOPSIS

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

DESCRIPTION

       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.

OPTIONS

       -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.

FEEDBACK

   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.

         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>

COPYRIGHT

       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.