[Bioperl-l] PAML + Codeml problem..

Chris Fields cjfields at uiuc.edu
Fri Aug 11 11:42:04 EDT 2006


Just so everyone knows, (and it's probably unrelated to all this), but
several enhancement requests were added recently to Bio::Tools::Phylo::PAML
in CVS. The notes for these are in Bugzilla and have to do with parsing
models in codeml output:

http://bugzilla.open-bio.org/show_bug.cgi?id=1883

http://bugzilla.open-bio.org/show_bug.cgi?id=2054

http://bugzilla.open-bio.org/show_bug.cgi?id=2055

Chris 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Torsten Seemann
> Sent: Thursday, August 10, 2006 5:11 PM
> To: golharam at umdnj.edu
> Cc: bioperl-l at lists.open-bio.org; 'Xianjun Dong'
> Subject: Re: [Bioperl-l] PAML + Codeml problem..
> 
> > 1.  The Bio::Seq::translate function (to my knowledge) only uses the
> > generic codon table.  So, you will need to translate the DNA sequence
> > using some other method.
> 
> Actually, the translate() method has a (-codontable_id => ??) parameter:
> 
> http://doc.bioperl.org/bioperl-live/Bio/PrimarySeqI.html#POD10
> 
> Here are the table IDs:
> 
> http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
> 
> --
> Torsten Seemann
> Victorian Bioinformatics Consortium, Monash University, Australia
> http://www.vicbioinformatics.com/
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



More information about the Bioperl-l mailing list