[Bioperl-l] use CLUSTALW on Windows?

Jason Stajich jason at bioperl.org
Thu Apr 30 13:31:19 EDT 2009


the bioperl-run module of Bio::Tools::Run::Alignment::Clustalw or  
MUSCLE ones don't work then? They do the cmdline work for you.

On Apr 30, 2009, at 9:52 AM, Jon Flowers wrote:

>
> Hi,
>
> There is no means to do this in bioperl, but it is simple to make a  
> system
> call and execute an MSA program such as MUSCLE to align fasta- 
> formatted
> sequences using something like...
>
> qx(muscle -in $infilename -out $outfilename)
>
> Jonathan
>
>
> laxmanb wrote:
>>
>> I need to create a multiple sequence alignment of some sequences  
>> using
>> CLUSTALW or any other Multiple sequence alignment program. However,  
>> I've
>> learnt that this functionality used to be UNIX/Linux only. However,  
>> the
>> documentation is also very old, so I'd like to know if any CLUSTAL/  
>> any
>> other MSA programs can be run using BioPerl on Windows.
>>
>> Thank you for your time :)
>>
>
> -- 
> View this message in context: http://www.nabble.com/use-CLUSTALW-on-Windows--tp23264714p23320232.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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Jason Stajich
jason at bioperl.org





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