Multiple Alignment of DNA Sequences with MAFFT

  • Kazutaka Katoh
  • George Asimenos
  • Hiroyuki Toh
Part of the Methods in Molecular Biology book series (MIMB, volume 537)


Multiple alignment of DNA sequences is an important step in various molecular biological analyses. As a large amount of sequence data is becoming available through genome and other large-scale sequencing projects, scalability, as well as accuracy, is currently required for a multiple sequence alignment (MSA) program. In this chapter, we outline the algorithms of an MSA program MAFFT and provide practical advice, focusing on several typical situations a biologist sometimes faces. For genome alignment, which is beyond the scope of MAFFT, we introduce two tools: TBA and MAUVE.

Key words

Multiple sequence alignment progressive method iterative refinement method consistency objective function genome comparison 



We thank Chuong B. Do for critical reading of the manuscript.


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Kazutaka Katoh
    • 1
  • George Asimenos
    • 2
  • Hiroyuki Toh
    • 3
  1. 1.Digital Medicine InitiativeKyushu UniversityFukuokaJapan
  2. 2.Department of Computer ScienceStanford UniversityStanfordUSA
  3. 3.Medical Institute of BioregulationKyushu UniversityFukuokaJapan

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