[Bioperl-l] Trouble with Clustalw

[Chris Fields]

On Aug 7, 2009, at 4:19 AM, Peter wrote:

> On Thu, Aug 6, 2009 at 9:25 PM, Chris Fields<cjfields at illinois.edu>  
> wrote:
>> Michael,
>>
>> Are you using ClustalW 2?  I'm not sure but I don't think the  
>> wrapper has
>> been updated for the latest version (I think parsing still works,  
>> though).
>>
>> chris
>
> That shouldn't matter, according to Des Higgins ClustalW 2 is intended
> to be completely compatible with ClustalW 1.83, including the command
> line options. They will be adding new stuff in ClustalW 3. The only
> think to worry about with ClustalW 2 is parsing the output, as the
> header line of the alignments has changed very slightly.
>
> I can tell you from personal experience that the Biopython command
> line wrappers for ClustalW work fine on both 1.83 and 2.0.10 for
> example, and would expect the same to be true for BioPerl.
>
> Peter

I would think so as well, but I encountered some issues on my OS using  
ClustalW 2 with the last release:

http://bugzilla.open-bio.org/show_bug.cgi?id=2728

I think it's something small, like something hard-coded in (version  
maybe) that's causing the problem, just didn't have time to check.

chris