MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

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 im...

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Bibliographic Details
Published in:	Molecular biology and evolution Vol. 30; no. 4; pp. 772 - 780
Main Authors:	Katoh, Kazutaka, Standley, Daron M.
Format:	Journal Article
Language:	English
Published:	United States Society for Molecular Biology and Evolution 01.04.2013 Oxford University Press
Subjects:	Algorithms Amino Acid Sequence Base Sequence DNA, Fungal - genetics DNA, Ribosomal - genetics DNA, Ribosomal Spacer - genetics Fast Tracks Fungi - genetics Humans Models, Genetic Molecular biology Molecular Sequence Data Phylogeny Protein Structure, Tertiary Proteins Quality Improvement Ribonucleases - chemistry Ribonucleases - genetics Ribosome Subunits, Small, Bacterial - genetics RNA, Bacterial - genetics Sequence Alignment - methods Software Transcription Factors protein structure metagemone progressive alignment parallel processing multiple sequence alignment
ISSN:	0737-4038, 1537-1719, 1537-1719
Online Access:	Get full text
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Abstract	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.
AbstractList	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.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. 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. 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. [PUBLICATION ABSTRACT]
Author	Katoh, Kazutaka Standley, Daron M.
AuthorAffiliation	1 Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan 2 Computational Biology Research Center, The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
AuthorAffiliation_xml	– name: 2 Computational Biology Research Center, The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan – name: 1 Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
Author_xml	– sequence: 1 givenname: Kazutaka surname: Katoh fullname: Katoh, Kazutaka email: kazutaka.katoh@aist.go.jp – sequence: 2 givenname: Daron M. surname: Standley fullname: Standley, Daron M.
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/23329690$$D View this record in MEDLINE/PubMed
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ContentType	Journal Article
Copyright	The Author 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2013 Copyright Oxford Publishing Limited(England) Apr 2013
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Keywords	protein structure metagemone progressive alignment parallel processing multiple sequence alignment
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Snippet	We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned...
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SubjectTerms	Algorithms Amino Acid Sequence Base Sequence DNA, Fungal - genetics DNA, Ribosomal - genetics DNA, Ribosomal Spacer - genetics Fast Tracks Fungi - genetics Humans Models, Genetic Molecular biology Molecular Sequence Data Phylogeny Protein Structure, Tertiary Proteins Quality Improvement Ribonucleases - chemistry Ribonucleases - genetics Ribosome Subunits, Small, Bacterial - genetics RNA, Bacterial - genetics Sequence Alignment - methods Software Transcription Factors
Title	MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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