[Biopython] triple align

[Peter Cock]

Not within Biopython alone, no.

I would do a codon-aware alignment by aligning the protein sequence
(e.g. with MUSCLE), and then "back-translate" the amino acids to the
original codons by threading the original nucleotide sequence onto the
protein alignment.

You can do that part within Biopython, here's a script of mine for this
with a wrapper for use within Galaxy:

https://github.com/peterjc/pico_galaxy/blob/master/tools/align_back_trans/align_back_trans.py

(Right now this does not have a proper command line API)

Peter

On Wed, Apr 12, 2017 at 10:14 AM, 李团 <imlituan at gmail.com> wrote:
> I want to align my amino acid sequence using triple as a unit, like 'ATT' is
> treated as one unit, is this possible in biopython?
>
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