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