[Bioperl-l] informative codons method for kaks -- Bio/Align/DNAStatistics.pm

Albert Vilella avilella at gmail.com
Thu Aug 17 07:37:20 EDT 2006


Hi all,

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, AFAICS, 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 do you think? Jason? Chris?

http://bugzilla.open-bio.org/show_bug.cgi?id=2078

Bests,

    Albert.




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