Massive parallelization of MUSCLE on a CUDA GPU.

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See how you use it in the How to use section.

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Requires the CUDA SDK and Visual Studio 2010 installed.

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This program is the outcome of our Master's Thesis.


This thesis examines the possibilities of parallel execution of the multiple sequence alignment program, MUSCLE, after which this is implemented using a graphic card with CUDA to carry out the parallel execution of the algorithms.

The implementation is being tested for the best possible optimizations and the best setup, after which these is being fixed in the implementation. Hereafter it is being examined how fast MUSCLE has become, and in which cases the algorithm is faster than the original implementation on CPU.

The result of these studies and other important information, which was determined during the process, is summarized in the thesis. Among other things, we find out that our implementation of MUSCLE with CUDA is 99.5 faster than the original implementation when run with 5 sequences which are 18,000 characters long each.

This version of MUSCLE is used in exactly the same way as the original. Just specify the argument -Cuda, when you run it. If you do not specify this, then the original version of MUSCLE is executed.

It is based on version 3.8.31 of the original MUSCLE.

If you have any question about the software, please do not hesitate to contact us.