[Bioperl-l] Bio::PopGen::Utilities->aln_to_population

Jason Stajich jason at bioperl.org
Thu Jan 22 06:13:03 UTC 2009

It isn't clear what version of BioPerl you are actually using - The  
version of Perl is independent of the version of BioPerl.  The current  
version has the 'codon' method which basically just makes  
"Markers" (or "Sites") as codons instead of single nucleotides.

You should get the latest version of BioPerl - 1.6 is about to go out  
the door very very soon (few days), you can find information at the  
website  http://bioperl.org

There is some syn/nonsyn codon calling is done in the mcdonald  
kreitman implementation Bio::PopGen::Statistics  see the  
mcdonald_kreitman method.

There is also code for calling a change synonymous/nonsynomous etc in  
a couple of different of modules Bio::Align::DNAStatistics has some  
Ka, Ks code and the Bio::MolEvol::CodonModel provides a method to  
calculate the ns and syn changes between two codons.

Undoubtably there needs  to be some more examples and documentation of  
how to use all these resources on molecular evolution front but it as  
been at the back of the queue for a while.

Hope that helps,

On Jan 21, 2009, at 3:49 PM, Andy Reynolds wrote:

> Hi Jason,
> I'd like to use this method with the 'codon' site model for annotating
> synonymous/non-synonymous snps but I'm unable to do this with the BIO
> packages installed under perl v 5.8.6.  Can you tell me which  
> version of
> Bioperl supports this functionality?
> Many thanks in advance.
> Andy

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