[Python-Dev] Questions about Codon Alignment Proposal (original) (raw)

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: http://lists.open-bio.org/pipermail/biopython-dev/2013-April/010560.html

(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 communities.)

Thanks,

Peter

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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