Multiple alignment of DNA sequences with MAFFT

Methods Mol Biol. 2009;537:39-64. doi: 10.1007/978-1-59745-251-9_3.

Abstract

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.

MeSH terms

  • Algorithms*
  • Animals
  • Base Sequence
  • Computational Biology / methods
  • Humans
  • Molecular Sequence Data
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*
  • Software*