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.

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