[Biopython-dev] Questions about Codon Alignment Proposal

[Peter Cock]

On Sat, Apr 27, 2013 at 6:23 PM, 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?

I'm not sure what Eric had in mind, but one option is to wrap an
existing specialised tool specifically for model selection. One
example I can think of is the graphical tool Topali2 (written by
some of my current work colleagues) which I believe initially
called Modelgenerator to do this, but now calls PhyML:

http://www.topali.org
http://bioinf.nuim.ie/modelgenerator/

> 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

Again, you'd have to ask Eric exactly what he had in mind.

Both these questions would probably be idea to ask on the
NESCent Google Group - there should be some phylogenetic
experts able to give a much more detailed answer than I can :)
https://plus.google.com/communities/105828320619238393015

Peter