Question: Multicore Support for Muscle
0
gravatar for branch.lizard
4.4 years ago by
branch.lizard0 wrote:

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?

alignment • 3.6k views
ADD COMMENTlink modified 2.8 years ago by Biostar ♦♦ 20 • written 4.4 years ago by branch.lizard0

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

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

ADD REPLYlink written 4.4 years ago by natasha.sernova3.8k
3
gravatar for Pappu
4.4 years ago by
Pappu1.9k
Pappu1.9k wrote:

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

ADD COMMENTlink written 4.4 years ago by Pappu1.9k

Have you had any luck with gnu parallel?

ADD REPLYlink written 4.4 years ago by branch.lizard0
2

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..

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by 5heikki9.1k
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