[Bioperl-l] Bio::Tools::Run::Alignment::Clustalw

[Barry Moore]

Angshu-

I was under the mistaken impression that clustalw wasn't ported to
Windows (I thought clustalx was the only Windows option).  Clearly this
is not the case, so disregard my previous reply to your e-mail.  If you
don't already have them, the binaries for clustalw for Windows are here:
ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/.

Barry

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Scott Markel
Sent: Friday, October 14, 2005 3:45 PM
To: Angshu Kar
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Bio::Tools::Run::Alignment::Clustalw

Angshu,

I run ClustalW on Windows via BioPerl, but inside our data
pipelining product.

The BioPerl-related lines that I use are

$ENV{CLUSTALDIR} = $clustalDirectory;
my @parameters = ("dnamatrix" => $dnaMatrix,
                   "gapopen"   => $gapOpeningPenalty,
                   "gapext"    => $gapExtensionPenalty,
                   "matrix"    => $proteinMatrix,
                   "outfile"   => $outputFile);
my $clustalFactory =
Bio::Tools::Run::Alignment::Clustalw->new(@parameters);
my $alignment = $clustalFactory->align($fastaFile);

Let me know if you need more context.

Scott

Angshu Kar wrote:

> Hi,
>  Has anyone used Bio::Tools::Run::Alignment::Clustalw in Windows? If
so,
> could you please let me know the steps for running the tool for a
seq.fafile?
>  Thanks,
> Angshu
> 
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> 
> 

-- 
Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at scitegic.com
SciTegic Inc.                       mobile: +1 858 205 3653
9665 Chesapeake Drive, Suite 401    voice:  +1 858 279 8800, ext. 253
San Diego, CA 92123                 fax:    +1 858 279 8804
USA                                 web:    http://www.scitegic.com

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