MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform

Kazutaka Katoh, Kazuharu Misawa, Kei Ichi Kuma, Takashi Miyata

Research output: Contribution to journalArticlepeer-review

9266 Citations (Scopus)


A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homologous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT.The performances of FFT-NS-2 and FFT-NS-1 were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.

Original languageEnglish
Pages (from-to)3059-3066
Number of pages8
JournalNucleic acids research
Issue number14
Publication statusPublished - 2002 Jul 15
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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