[Bioperl-l] PAML + Codeml problem..

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Thu Aug 10 18:11:15 EDT 2006


> 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/


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