[Bioperl-l] Bioperl "align is not recognized as internal or external command"

[anikng at gmail.com]

Hi Forum members,

My purpose is to do multiple sequence alignment using perl script and 
Bioperl mdules. For that I installed Bioperl  and Clusalw2 (2.1) in my 
Windows 7. When i tried to run a small code (attached below), it is showing 
some error
as "align is not recognized as internal or external command etc etc.. A 
screen shot is attached.

I saw someone post similar error, but could not find any solution. So, 
kindly suggest me the solution.


An Lee, Seoul,
ROK



Code,

#!/usr/bin/perl
use Bio::Seq;
use Bio::Tools::Run::Alignment::Clustalw; 
use Bio::AlignIO;

BEGIN { $ENV{CLUSTALDIR} = 'C:/ClustalW2/clustalw2.exe'} 
 
$factory = Bio::Tools::Run::Alignment::Clustalw->new(-matrix => 'BLOSUM');
$ktuple = 3;
$factory->ktuple($ktuple);  # change the parameter before executing
 
$in="1.fasta";
$aln = $factory->align($in);

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