[Biopython] clustalW output format

[Stefanie Lück]

Thanks Peter!

I'm also using version 2.1. I didn't check the -help, only the homepage
where they say "Default value is: Aln w/numbers [aln1]", which confused
me...
Thanks for mentioning Clustal Omega, I didn't know that say changed the
names.
Stefanie

-----Ursprüngliche Nachricht-----
Von: Peter Cock [mailto:p.j.a.cock at googlemail.com] 
Gesendet: Dienstag, 2. August 2011 16:55
An: Stefanie Lück
Cc: biopython at lists.open-bio.org
Betreff: Re: [Biopython] clustalW output format

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