Multithreading Clustalw On Amazon Ec2

Question

[User 7351]

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

Answer 1

[Andreas]

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