mafft

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 9:286-298) 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.