BP_PAIRWISE_KAKS(1p)					User Contributed Perl Documentation				      BP_PAIRWISE_KAKS(1p)

NAME

       pairwise_kaks - script to calculate pairwise Ka,Ks for a set of sequences

SYNOPSIS

       pairwise_kaks.PLS -i t/data/worm_fam_2785.cdna [-f fasta/genbank/embl...] [-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 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.

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/wiki/Mailing_lists	- About the mailing lists

   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://redmine.open-bio.org/projects/bioperl/

AUTHOR

	Jason Stajich jason-at-bioperl-dot-org

perl v5.14.2							    2012-03-02						      BP_PAIRWISE_KAKS(1p)