[Bioperl-guts-l] [BioPerl - Feature #2078] informative codons method for kaks -- Bio/Align/DNAStatistics.pm

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Wed Mar 30 14:41:25 EDT 2011


Issue #2078 has been updated by Chris Fields.

Tracker changed from Bug to Feature


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Feature #2078: informative codons method for kaks -- Bio/Align/DNAStatistics.pm
https://redmine.open-bio.org/issues/2078

Author: Albert Vilella
Status: New
Priority: Low
Assignee: Bioperl Guts
Category: Core Components
Target version: main-trunk
URL: 


I think it would be nice to have a method in
Bio/Align/DNAStatistics.pm that gives the number of informative codons
for kaks in a MSA. That is, the codons that are used in the
calculation of kaks. This, AFAIK, more or less what codeml calls
"patterns".

I often find myself in the situation of wanting to know how big is the
CDS alignment not in terms of sequence length, but of the number of
codons that are going to be used in the kaks statistics. I guess this
method would help in that.

The method could:

return the number of informative codons?
maybe return a new seqarray with only the informative codons?

What you reckon? Jason? Chris?


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