[Biopython] clustalW output format

[Peter Cock]

On Tue, Aug 2, 2011 at 2:15 PM, Stefanie Lück <lueck at ipk-gatersleben.de> wrote:
> Hello!
>
> I’m using ClustalW2 for my alignments and would like to have the aln1 output
> format (http://www.ebi.ac.uk/Tools/msa/clustalw2/help/). This should show
> the line numbers. Actually this should be the default but it’s not.

I have version 2.1 installed and the default output format is traditional
Clustal output with no residue/base numbers (according to -help).

Which version of ClustalW2 are you using?

I'm expecting we'll need a new wrapper for Clustal Omega (I don't know
why they didn't call it Clustalw v3).

We'll probably also need to update Clustalw parser to cope with base/residue
numbering in the output as well.

Peter