[Biopython] Codeml parser in Biopython?

[Peter]

On Mon, Sep 13, 2010 at 5:22 PM, natassa <natassa_g_2000 at yahoo.com> wrote:
> Hello,
> I was wondering if there  is a Biopython solution to parsing codeml results from
> paml. the output files are pretty standard, so such a parser should be quite
> straightforward to write up. I d volunteer for this, but thought I might check
> first if somebody else has done this. Actually, I found a read-only pypaml
> interface in google codes, tried it out and realized I had to edit several
> things to even import it (in python 2.5), which is quite strange: It was mainly
> built-in methods that throwed errors..Anyway, i 'corrected' this and then
> realized that the output files assumed by this code may not be the same as mine,
> although again, the outputs of codeml are pretty standard. I am not sure how
> much this code is used and was not sure what is the developper's email to ask
> him some questions.
>
> I am interested in parsing outputs from Branch, Site and BranchSite models, so
> everthing that codeml can do. Any information by experienced users is welcome!
> Thanks,
> Anastasia Gioti

Hi Anastasia,

Could you post a short example of the kind of output you are looking at?

Can you get codeml to output what you need in another format, such as NEXUS?

Peter