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Gmane
From: <anikng <at> gmail.com>
Subject: Bioperl "align is not recognized as internal or external command"
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Thursday 1st May 2014 04:47:22 UTC (over 2 years ago)
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);
 
CD: 12ms