MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc. Visit the program website and check /usr/doc/mafft-* for citing and licensing informations: this program is released under a BSD license but its extensions use different ones.