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

[Scott Markel]

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
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