MUSCLE is public domain multiple alignment software for protein and nucleotide sequences. MUSCLE stands for multiple sequence comparison by log-expectation.
To perform an alignment using MUSCLE, select the sequences or alignment you wish to align and select Align/Assemble → Multiple Align.... Select MUSCLE as the alignment type, and the options available for a MUSCLE alignment will be displayed.
For more information on muscle and its options, please refer to the original documentation for the program: http://www.drive5.com/muscle/muscle.html.