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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Summary: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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Associate editor: Sudhir Kumar
ISSN:0737-4038
1537-1719
1537-1719
DOI:10.1093/molbev/mst010