debian man page for bp_pairwise_kaks

Query: bp_pairwise_kaks

OS: debian

Section: 1p

Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar

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)
Related Man Pages
bp_aacomp(1p) - debian
bp_pairwise_kaks(1p) - debian
bp_parse_hmmsearch(1p) - debian
bio::seqfeature::gene::promoter(3pm) - debian
bio::seqio::tigrxml(3pm) - debian
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