Question: Multithreading Clustalw On Amazon Ec2
1
gravatar for User 7351
7.0 years ago by
User 735140
User 735140 wrote:

I just got acquainted with Amazon EC2 and need to conduct some rather large alignments. Unfortunately, each alignment uses only one out of 8 cores in my 20 unit extra large processing instance. I found ClustalW-MTV at

http://www4a.biotec.or.th/GI/tools/clustalw-mtv

and am wondering if anyone has experience using this software or has another solution for me.

Thanks,

Jared

alignment clustalw • 1.9k views
ADD COMMENTlink written 7.0 years ago by User 735140
1
gravatar for Andreas
7.0 years ago by
Andreas2.4k
Singapore
Andreas2.4k wrote:

It depends a bit how long your sequences are and if they are protein or nucleic acid, but you might want to try Clustal Omega or MAFFT instead of ClustalW. Clustal Omega is designed to be able to compute really large alignments (>100k) and it can use multiple cores, at least during the pairwise alignment stage, just like MAFFT.

Andreas

ADD COMMENTlink modified 7.0 years ago • written 7.0 years ago by Andreas2.4k
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