Multicore Support for Muscle

Question

[branch.lizard]

I am searching for a multicore solution to multiple sequence alignment using MUSCLE. I would really like to stay with MUSCLE rather than an alternative alignment tool; however, the performance seems to be a major pitfall. Does anyone know how to run MUSCLE to utilize more than one CPU core/thread?

If not, would anyone like to suggest an alternative alignment tool which performs as well at alignments as MUSCLE, but has multicore support?

[natasha.sernova]

Mafft should be OK, as Pappu wrote.. Its web site is below:

http://mafft.cbrc.jp/alignment/software/

Answer 1

[Pappu]

You can try mafft. Muscle algorithm is hard to parallelize.

[branch.lizard]

Have you had any luck with gnu parallel?

[5heikki]

GNU parallel makes it easy to run multiple instances of muscle in parallel (e.g. aligning 4 different files in parallel). It can't magically parallelize single-threaded programs though..