May 26, 2018
Multiple alignment program for amino acid or nucleotide sequences
MAFFT offers a range of multiple alignment strategies, L-INS-i accurate; recommended for <200 sequences, FFT-NS-i standard speed and accuracy, FFT-NS-2 fast; recommended for >2,000 sequences, etc. According to BAliBASE and other benchmark tests, L-INS-i is one of the most accurate methods currently available.
MAFFT has been described
K. Katoh and H. Toh 2008 Briefings in Bioinformatics 9286-298 Recent developments in the MAFFT multiple sequence alignment program.
K. Katoh, K. Misawa, K. Kuma and T. Miyata Nucleic Acids Res. 30 3059-3066, 2002 MAFFT a novel method for rapid multiple sequence alignment based on fast Fourier transform.