anikng | 1 May 06:47 2014
Picon

Bioperl "align is not recognized as internal or external command"

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);

_______________________________________________
Bioperl-l mailing list
Bioperl-l <at> lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

Gmane