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.\"
.IX Title "BP_PAIRWISE_KAKS 1p"
.TH BP_PAIRWISE_KAKS 1p "2017-08-30" "perl v5.26.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
bp_pairwise_kaks \- script to calculate pairwise Ka,Ks for a set of sequences
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
bp_pairwise_kaks.PLS \-i t/data/worm_fam_2785.cdna [\-f fasta/genbank/embl...] [\-msa tcoffee/clustal] [\-kaks yn00/codeml]
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
.Vb 5
\&  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 ML
\& method of Yang with the PAML package.
\&
\& Requires:
\& * bioperl\-run package
\& * PAML program codeml or yn00
\& * Multiple sequence alignment programs Clustalw OR T\-Coffee
\&
\& Often there are specific specific parameters you want to run when you
\& a computing Ka/Ks ratios so consider this script a starting point and
\& do not rely it on for every situation.
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
.Vb 1
\& Jason Stajich jason\-at\-bioperl\-dot\-org
.Ve