Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 30, Issue 4, Pages 772-780Publisher
OXFORD UNIV PRESS
DOI: 10.1093/molbev/mst010
Keywords
multiple sequence alignment; metagemone; protein structure; progressive alignment; parallel processing
Funding
- Platform for Drug Discovery, Informatics, and Structural Life Science from the Ministry of Education, Culture, Sports, Science and Technology, Japan
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Japan
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We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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