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UGENE contains graphical ports of the Robert C. Edgar’s MUSCLE tool for multiple alignment.

MUSCLE4 is not supported since UGENE version 1.7.2.

The package is integrated completely, so there is no need in extra files for using it. It is possible to run several multiple alignment tasks in parallel, check the progress and cancel the running tasks safely.

The k-mer clustering part of the MUSCLE algorithm was optimized for multicore systems by Timur Tleukenov, Novosibirsk State Technical University.

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