Multiple Sequence Alignment Methods

Volume 1079 of the series Methods in Molecular Biology pp 131-146


MAFFT: Iterative Refinement and Additional Methods

  • Kazutaka KatohAffiliated withImmunology Frontier Research Center, Osaka UniversityComputational Biology Research Center, The National Institute of Advanced Industrial Science and Technology (AIST)
  • , Daron M. StandleyAffiliated withImmunology Frontier Research Center, Osaka University

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This chapter outlines several methods implemented in the MAFFT package. MAFFT is a popular multiple sequence alignment (MSA) program with various options for the progressive method, the iterative refinement method and other methods. We first outline basic usage of MAFFT and then describe recent practical extensions, such as dot plot and adjustment of direction in DNA alignment. We also refer to MUSCLE, another high-performance MSA program.

Key words

Multiple sequence alignment Iterative refinement Fast Fourier transform Metagenome Protein structure