[Bioperl-l] questions on analysising clustalw alignment result files

[Chris Fields]

On Jul 5, 2011, at 8:50 AM, Peter Cock wrote:

> On Tue, Jul 5, 2011 at 11:50 AM, Tao Zhu <tzhu at mail.bnu.edu.cn> wrote:
>> I've created an alignment file using clustalw 2.0.12. This file "test.aln"
>> is attached in the mail.
>> 
>> I want to analysis it using Bio::AlignIO, ...
> 
> The Biopython clustal parser doesn't like it either - I think the extra sequence
> numbers are the problem, I don't recall seeing those with clustalw 2.0.10.
> 
> I just checked and there is already a clustalw 2.1 release, and a new
> release Clustalw Omega 1.0.2 (which curiously isn't called clustalw v3).
> 
> Peter

The best thing to do in this case is to file a bug for tracking (might be a good thing to have cross-lang bugs in this case, maybe?).  Anyway, it's very likely as Peter says, the parser is choking on something and doesn't recognize the file.

chris