hello everybody, i just installed perl, bioperl and clustalw. I have near one year from the last time i worked with perl. Too many errors not leeting me use bioperl modules stopped me back then fromm keeping up with perl.No i m here again and i want your help. i have a quite easy task for a monk, but for a newbie like me its a bit tricky.All i have to do is a multile allingnment of a protein fasta file using clustalw.

#!/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 => 'BL
+OSUM');
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);

[download]

Cant see if this code actually Works,beacause of this anoynig message :Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (you may need to install the Bio::Tools::Run::Alignment::Clustalw module) (@INC contains: C:/Perl64/site/lib C:/Perl64/lib .) at c3.pl line 8. BEGIN failed--compilation aborted at c3.pl line 8.

Any help will be much apreciated!Its extremely important to finish my task by any means as soon as possible

In reply to Clustalw and bioperl by dimitris852

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