[Biopython-dev] [Biopython - Feature #3338] (New) Convert a protein alignment and nucleotide sequences to codon alignment

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Issue #3338 has been reported by Eric Talevich.

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Feature #3338: Convert a protein alignment and nucleotide sequences to codon alignment
https://redmine.open-bio.org/issues/3338

Author: Eric Talevich
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


As discussed on the mailing list:
http://lists.open-bio.org/pipermail/biopython/2012-April/007913.html

This could be implemented in two ways:
1. Wrap PAL2NAL (pal2nal.pl) under Bio.Align.Applications
2. Implement this functionality directly in Python

While PAL2NAL has some convenience features like aligning protein sequences to CDS sequences that don't exactly match, it would be straightforward (and simpler for the user, in most cases) to implement a fussier version of it from scratch somewhere in Biopython.

So, where would be put this function?

Related:
* From a codon alignment, it would again be straightforward to calculate dN/dS ratios for pairs of sequences, much like PAML's yn00 (although that program does more stuff, too). Do we want to do that? Where?
* Are there ways Biopython could support codon alignments better, as distinct from nucleotide alignments?


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