MAFFT (Multiple Alignment with Fast Fourier Transform) is a multiple sequence alignment program. MAFFT implements the Fast Fourier Transform (FFT) to optimize protein alignments based on physical properties of the amino acids. The program uses progressive alignment and iterative alignment. Nucleotide and amino acid sequences in FASTA format can be aligned. MAFFT is useful for hard-to-align sequences such as those containing large gaps (e.g., rRNA sequences containing variable loop regions)
Parent program: mafft
MAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences that uses fast Fourier transform and simplified scoring system to rapidly identify homologous regions between sequences. MAFFT performs well in reducing CPU time required for multiple sequence alignment and allows an increased the accuracy of alignments even for sequences with large insertions or extensions as well as distantly related sequences of similar length. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of < 200 sequences), FFT-NS-2 (fast; for alignment of < 30,000 sequences), etc. The type of input sequences (amino acid or nucleotide) is automatically recognized.