Multiple Alignment using Fast Fourier Transform

Other names: MAFFT

MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program which implements the Fast Fourier Transform (FFT) to optimise protein alignments based on the physical properties of the amino acids. The program uses progressive alignment and iterative alignment. MAFFT is useful for hard-to-align sequences such as those containing large gaps (e.g., rRNA sequences containing variable loop regions).