uMUSCLE
UGENE includes graphical interfaces for Robert C. Edgar’s MUSCLE tool for multiple alignments.
MUSCLE4 is not supported since UGENE version 1.7.2.
The package is fully integrated, so there is no need for additional files to use it. You can execute multiple alignment tasks in parallel, check their progress, and safely cancel running tasks.
The k-mer clustering component of the MUSCLE algorithm was optimized for multicore systems by Timur Tleukenov from Novosibirsk State Technical University.