MAFFT is a fast multiple sequence alignment program for aminoacids and nucleotids. According to number of sequences and demands to time and accuracy 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.
mafft-7.313: MAFFT version 7.313, 64-bit, Intel compiler
mafft-7.305: MAFFT version 7.305, 64-bit, Intel compiler
mafft-7.273: MAFFT version 7.273, 64-bit, Intel compiler
mafft-7.029: MAFFT version 7.029, 64-bit
module add mafft-7.313
mafft [arguments] input > output
Free for academic users