[Python-Dev] Questions about Codon Alignment Proposal

Peter Cock p.j.a.cock at googlemail.com
Sat Apr 27 22:04:02 CEST 2013

Hi Guido,

Yes indeed, wrong list - I've forwarded this to the intended destination,
biopython-dev, and we'll continue the discussion there:

(It is nice to see Python getting used in all sorts of Google Summer
of Code projects though - and I'm sure we're all keen to try and
welcome and encourage new students to the different open source



On Sat, Apr 27, 2013 at 6:36 PM, Guido van Rossum <guido at python.org> wrote:
> Sounds like this was accidentally CC'ed to python-dev.
> On Sat, Apr 27, 2013 at 10:23 AM, 阮铮 <rz1991 at foxmail.com> wrote:
>> Hi Eric and Peter,
>> I'm preparing the proposal for the codon alignment project. Two things I may
>> want to hear your advice.
>> 1) In the biopython wiki page, you mentioned "model selection" in the
>> Approach & Goals. I'm not sure if there are any advantages to use codon
>> alignment for model selection. Could you give me some references? Another
>> thing is that model selection involves estimation of tree topology as well
>> as branch lengthes and parameters across many substitution models. Will it
>> be too computationally intensive for a python implementation?
>> 2) You also mentioned the "validation (testing for frame shift)". Is there a
>> test for frame shift? Or I can simply detect it by comparing amino acid
>> sequences and nucleotide sequences.
>> Best,
>> Zheng Ruan
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> --
> --Guido van Rossum (python.org/~guido)

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