[Biopython-dev] Fwd: Questions about Codon Alignment Proposal

[Peter Cock]

Oops - biopython-dev != python-dev ;)

(I'll reply shortly)

Peter

---------- Forwarded message ----------
From: 阮铮 <rz1991 at foxmail.com>
Date: Sat, Apr 27, 2013 at 6:23 PM
Subject: Questions about Codon Alignment Proposal
To: Eric Talevich <eric.talevich at gmail.com>, "p.j.a.cock"
<p.j.a.cock at googlemail.com>
Cc: python-dev <python-dev at python.org>


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