[Bioperl-l] Clustalw module

Nathan Haseley (RIT Student) nsh9351 at rit.edu
Wed Jul 2 10:34:51 EDT 2008

   I am working with the Bioperl module Bio::Tools::Run::Alignment::Clustalw.  I try to include the package in my script as follows:

use Bio::Seq;
use Bio::SearchIO;
use Bio::Tools::Run::StandAloneBlast;
use Bio::DB::GenBank;
use Bio::Tools::Run::Alignment::Clustalw;
use Bio::Root::Exception;
use Error qw(:try);

but I keep getting the following error message:
Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl .) at ./BlastTwoCompare.pl line 6.
BEGIN failed--compilation aborted at ./BlastTwoCompare.pl line 6.

The Clustalw program is configured correctly to work in my directory.  Am I missing something obvious or is there something wrong with my BioPerl configuration?  Any advice on how to fix this?  Thank you for your time.


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