[Bioperl-l] Trouble with Clustalw

[Peter]

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