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Methods Mol Biol. 2014;1079:131-46. doi: 10.1007/978-1-62703-646-7_8.

MAFFT: iterative refinement and additional methods.

Author information

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

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.

PMID:
24170399
DOI:
10.1007/978-1-62703-646-7_8
[Indexed for MEDLINE]

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