[Python-Dev] Questions about Codon Alignment Proposal

Guido van Rossum guido at python.org
Sat Apr 27 19:36:40 CEST 2013

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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