Supported Applications


  • Description

    a multiple sequence alignment program for unix-like operating systems. 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).

  • Primary Citation*

    K. Katoh, K. Misawa, K. Kuma, and T. Miyata. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30(14): 3059-3066.
    (Note: describes the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies)

    • *Full citation information available through

  • Citation Note

    A full list of citations can also be found on the MAFFT website.

  • Webinars

    Topic: MAFFT/MAFFTash: Web services for structure-informed multiple sequence alignment
    Presenters: Kazutaka Katoh and Daron Standley, Immunology Frontier Research Center, Osaka University

    Host: Andrew Morin
    Recorded on July 17, 2014

  • Default Versions

    Linux 64:  7.429
    OS X INTEL:  7.429

  • Other Available Versions

      Linux 64:

      7.394, 7.313, 7.309
    • OS X INTEL:

      7.394, 7.313, 7.309
  • Developers

    Katoh Kazutaka.