How To Run Mauve In Multiple Core?
Entering edit mode
10.7 years ago
HG ★ 1.2k

Can anyone tell me how to run Mauve in multiple core through command line or else automatic parallelism will be done while it run??

Thank you advance.

Entering edit mode
10.6 years ago
Ben Lange ▴ 210

I'm no Mauve expert. In fact I hadn't heard about the package until this thread. Let's see if I can find anything useful.

As an overview, it sounds like Mauve has two main versions:

  • original: anchor and extend the default aligner is based on ClustalW and uses dynamic programming.

  • progressive: supports guide tree

After reading through the command line arguments, I'm not seeing anything that is multi-threading specific. I assume you're looking for max thread or core count parameters.

Reviewing the version history might be the answer you're looking for. The most recent update is from 11-11-2009. Known Issue: Parallelism has been disabled for all supported platforms to avoid a race condition bug. I'm assuming that once you run the tool, it will be obvious if single or multiple cores are getting used.

The point of using something like Mauve is to align several sequences in one go. If race conditions are a problem when the algorithm is in the same process, consider running the command line on chunks of your overall problem. Look for ways of generating intermediate files and then using those intermediate files as input to subsequent runs of the tool. If nothing else, there is an output-guide-tree option.

Thx, Ben


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