[Bioclusters] Parallel Sequence Alignment tool
jgans at lanl.gov
Tue Aug 25 11:04:35 EDT 2009
There is a nice paper from SGI on parallelizing the Clustal program
Even though this paper refers to an earlier version of Clustal (circa
2001), it is a very useful guide. Using this paper as a reference, it
was straight forward to add the required OpenMP code to the most recent
version of Clustal (I only modified the first stage pairwise alignment
portion of the code).
Bioscience Division, B-7
Los Alamos National Laboratory
Abhishek Pratap wrote:
> Hey Ognen
> Thanks for sharing. Just wondering if you could recommend anything
> good on how to convert single threaded programs into multiones.
> Ofcourse if the base algorithm is compatible. Any good resource that
> you would recommend ?
> On Mon, Aug 24, 2009 at 8:25 AM, Ognen Duzlevski<maketo at sdf.lonestar.org> wrote:
>> On Fri, 17 Jul 2009, slitster at rcn.com wrote:
>>> Date: Fri, 17 Jul 2009 10:41:53 -0400 (EDT)
>>> From: slitster at rcn.com
>>> Reply-To: HPC in Bioinformatics <bioclusters at bioinformatics.org>
>>> To: bioclusters at bioinformatics.org
>>> Subject: [Bioclusters] Parallel Sequence Alignment tool
>>> Does anyone have recommnedations for a parallel sequence alignment tool
>>> User investigation so far has turned up clustalW-MPI, but it seams to be
>>> using an older version of clustalW.
>> I once wrote a multi-threaded version of clustalw - you can get it here:
>> Bioclusters maillist - Bioclusters at bioinformatics.org
> Bioclusters maillist - Bioclusters at bioinformatics.org
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