Re: I can't access clustalw from my cgi perl program...

Since your script runs correctly from the command line, this doesn't look
like it's a BioPerl problem.

The error message you got is:

Can't locate Bio/Tools/Run/Alignment/Clustalw.pm

followed by a long list of directories where it looked for that module. So
the first thing to check is

Is Bio/Tools/Run/Alignment/Clustalw.pm in one of those @INC directories?

The fact that other Bioperl modules are 'use'd in your script first and
didn't produce an error suggests that you might have the BIoperl core
installation in those directories, but not Bio::Tools::Run.

If Bio/Tools/Run/Alignment/Clustalw.pm is in fact in the @INC directories
listed, then it's probably a CGI/web issue. Do you know as what user on your
machine web scripts are run? That user probably has limited permissions
compared to your regular user account.

Dave