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Multicore Support for Muscle

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
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updated by Biostar 380 • | written by branch.lizard 0

1 answer

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

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written by Pappu 210

Have you had any luck with gnu parallel?

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written by branch.lizard 0

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..

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written by 5heikki 1.1K

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