title: MAFFT: iterative refinement and additional methods.
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.
authors.affiliation: Immunology Frontier Research Center, Osaka University, Suita, Japan.
authors.forename: Kazutaka
authors.initials: K
authors.lastname: Katoh
authors.forename: Daron M
authors.initials: DM
authors.lastname: Standley
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003201:Computers; D004247:DNA / Q000235:genetics; D012313:RNA / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA; D004247:DNA