MUSCLE (multiple sequence comparison by log-expectation)'s public domain, multiple sequence alignment software for protein and nucleotide sequences. MUSCLE's often used as a replacement for Clustal, since it typically (but not always) gives better sequence alignments; in addition, MUSCLE 's significantly faster than Clustal, especially for larger alignments (Edgar 2004). MUSCLE's integrated into UGENE bioinformatics tool as a plugin.… (More on Muscle)