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Multiple Sequence Alignment Methods pp 131–146Cite as

MAFFT: Iterative Refinement and Additional Methods

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1079))

Abstract

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.

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Author information

Authors and Affiliations

  1. Immunology Frontier Research Center, Osaka University, Suita, Japan

    Kazutaka Katoh & Daron M. Standley

  2. Computational Biology Research Center, The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan

    Kazutaka Katoh

Authors
  1. Kazutaka Katoh
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  2. Daron M. Standley
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Editor information

Editors and Affiliations

  1. Dept. of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA

    David J Russell

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Katoh, K., Standley, D.M. (2014). MAFFT: Iterative Refinement and Additional Methods. In: Russell, D. (eds) Multiple Sequence Alignment Methods. Methods in Molecular Biology, vol 1079. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-646-7_8

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  • DOI: https://doi.org/10.1007/978-1-62703-646-7_8

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-645-0

  • Online ISBN: 978-1-62703-646-7

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