[BioPython] Calculating synonymous sites

[Jason Stajich]

Of course there are already a lot of existing programs out there to do
this...

We have a Nei-Gojoburi implementation in Bioperl
Bio::Align::DNAStatistics
if you want to adapt this to BioPython feel free.

Do you really need to code it yourself if you are new to programming or
can you rely on other programs?

HY-PHY and PAML have a ML calculation of Ka and Ks and can be scripted
with some work.

Kevin Thornton has a bunch of C++ code which does some of this as well
http://www.molpopgen.org/software/

-jason
On Fri, 17 Oct 2003 Sean.Maceachern at dpi.vic.gov.au wrote:

> Hello, I was hoping that someone may have run across an existing method
> for calculating the number of synonymous and non-synonymous sites. I am
> new at programming and I imagine it would take me a long time to code
> all of the possibilities etc.. so I was hoping someone might be able to
> offer some help or pass me on to an existing Biopython script before I
> begin, it seems like a lengthy process that someone must have done
> before.
>
> Cheers
>
> Sean MacEachern
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu