[Biopython-dev] Questions about Codon Alignment Proposal

[Saket Choudhary]

Hi Peter and Eric,

So do we also implement the alignment algorithm as well ? or do we use
clustalw or any other alignment software ?

Thanks
Saket

On 28 April 2013 03:55, Eric Talevich <eric.talevich at gmail.com> wrote:
> On Sat, Apr 27, 2013 at 4:11 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:
>
>> 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/
>>
>
> Actually, I added "model selection" to the project description because
> Peter mentioned it earlier. :)
>
> I didn't have any particular function in mind, but calling out to external
> tools sounds like a reasonable approach. We do have some primitive
> functionality for likelihood ratio testing through the PAML module, so
> maybe that could come into play here.
>
>> 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.
>>
>
> Yes, it's just a matter of testing for unexpected cases in which the
> protein and nucleotide sequences don't quite match, and handling them
> appropriately. It would be nice to see a description of these possible edge
> cases and your treatment of them in the detailed weekly schedule for the
> project.
>
>
>
>> 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
>>
>>
>
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