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

Jason Stajich jason at bioperl.org
Wed Jan 28 15:34:50 EST 2009


Good - I also added a syn and nonsync codon path calculation that is  
needed to support the mcdonald_kreitman test in Bio::MolEvol::CodonModel
  it may be possible to combine these, not sure.

-jason
On Jan 28, 2009, at 10:24 AM, Richard Harrison wrote:

> Hi all,
> I have updated the aln_to_population part of  
> Bio::PopGen::Statistics::Utilitities to include codon models for 4- 
> fold degenerate sites, synonymous, non-synonymous sites and also a  
> rough-n-ready indel excluder.... If you would like my script, (to  
> include or vet!) let me know..  I want to expand the PopGen side of  
> Bioperl  a bit further, as it doesn't do everything that I need at  
> the moment.
> Best wishes,
> Richard
>
>
>
> ____________________________
> Dr Richard Harrison
> richard.harrison at ed.ac.uk
> 127 Ashworth Labs
> Institutes of Evolutionary Biology
> King's Buildings
> West Mains Road
> Edinburgh EH9 3JT
>
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> Scotland, with registration number SC005336.
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Jason Stajich
jason at bioperl.org





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