[Biopython] "Appending" to an MSA

[Peter Cock]

On Tue, Jul 30, 2013 at 1:56 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
> Hello Eric,
>
> The functionality you are looking for does not exist in Biopython. Yet, as
> Peter suggests, there is command line hope for you:
>
> Clustal Omega
> http://www.clustal.org/omega/
>
> Specifically, see the documentation where it tells you how to align one or
> more sequences against a profile of pre-aligned sequences.
>
> Notice that nothing prevents you from running Clustal Omega as a subprocess
> from within Python. Actually, it works very well and you can read in its
> output from a PIPE using SeqIO.parse(...,'fasta').

And if you find it helpful, run clustalo via:

from Bio.Align.Application import ClustalOmegaCommandline
help(ClustalOmegaCommandline)

Peter