Trouble in running Clustalw in Bioperl

Question

[Andrea]

hello,I m trying to run clustalw in bioperl in order align a fasta file. I have installed the newer perl version and the newer bioperl version.

Code:

#!/usr/bin/perl

use warnings;
use strict;

use Bio::AlignIO;
use Bio::SeqIO;
use Bio::Tools::Run::Alignment::Clustalw;

my $file = shift or die; # Get filename from command prompt.
my $factory = Bio::Tools::Run::Alignment::Clustalw->new(-matrix => 'BLOSUM');
my $ktuple = 3;
$factory->ktuple($ktuple);

my $inseq = Bio::SeqIO->new(
                    -file => "<$file",
                    -format => $format
                   );

my $seq;
my @seq_array;
while ($seq = $inseq->next_seq) {
    push(@seq_array, $seq);
}

# Now we do the actual alignment.
my $seq_array_ref = \@seq_array;
my $aln = $factory->align($seq_array_ref);

I get the error:Can't locate Bioperl.pm in @INC (you may need to install the Bioperl module) (@INC contains: C:/Perl64/site/lib C:/Perl64/lib .) at c3.pl line 5. BEGIN failed--compilation aborted at c3.pl line 5.

So I assume there something going wrong with the insatalation of this module. Command: cpan install Bio::Tools::Run::Alignment::Clustalw has no good result. Any clue please? Is the code running on your system?

thanks so much!

[SES]

The error you posted was not generated by this code. Are you sure you are executing this script? The code looks fine.

[Andrea]

i have a broblem installing bioperl core package and bioperl-run package. Did you run the script in your system?