[Biopython] How can i use muscle to align with biopython?

[Peter]

On Mon, Aug 24, 2009 at 5:27 AM, Italo Maia<italo.maia at gmail.com> wrote:
> Ok, with clustal i import MultipleAlignCL and do_alignment and do the stuff,
> but where is the alignment modules for muscle?
> Using biopython 1.5.1 here with ubuntu 9.

That would be Biopython 1.51 (one, fifty-one). ;)

Also Ubuntu 9 is unclear, I guess you meant Ubuntu 9.04 ("Jaunty Jackalope")
which was released April 2009 (hence 9.04). Ubuntu releases are every six
months, so their next release should be October 2009, and is expected to be
called Ubuntu 9.10 ("Karmic Koala").

Anyway - thanks for answering about the alignments Andrew. To recap, to
call the alignment tools, use Bio.Align.Applications and Python module
subprocess, and then parse the resulting alignment file with Bio.AlignIO.
All in the tutorial :)

Bio.Clustalw is now semi-obsolete, but can expect a gradual retirement
(just like Bio.Fasta was gradually phrased out) because it was widely
used, and we don't want to force people to migrate their old code
immediately. I wouldn't recommend using Bio.Clustalw for new scripts,
try Bio.Align.Applications instead.

Regards,

Peter