MUSCLE stands for MUltiple Sequence Comparison by Log- Expectation. It uses kmer counting followed by a log expectation score profile function for progressive alignment in association with tree-dependant restricted partitioning. It can be obtained from http://www.drive5.com/muscle.
The basic format of a MUSCLE command is
muscle -in inputFile -out outputFile
Several flags can be added to allow for modification of the defaults. These are listed on several pages on the MUSCLE website: