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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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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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“We conducted the analysis twice (e.g. the GUIDANCE2 filter and subsequent PAML analysis) using different aligners: (1) Muscle version 3.8.31 (Edgar, 2004) and (2) Mafft version X7.721 (Katoh and Standley, 2013).”
From Genomic and physiological mechanisms underlying skin plasticity during water to air transition in an amphibious fish (2020) · cites this paper as Katoh and Standley, 2013
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“Because the alignments produced by BLS are very different from the ones produced by state-of-the-art software, such as MUSCLE version 5.1 (ref. 28) or MAFFT version 7.490 (ref. 29), it is difficult to fairly compare them as alignments.”
From Improving microbial phylogeny with citizen science within a mass-market video game (2025) · cites this paper as [29]
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“The three mutations in S1 (N501Y, A570D, ΔH69/V70) did not appear to impact neutralisation in a pseudovirus assay, consistent with data on N501Y having little effect on nuetralisation by convalescent and post vaccination sera40.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [40]
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Metadata
- Authors
- Katoh, K., & Standley, D. M.
- Affiliations
- Immunology Frontier Research Center, The University of Osaka (JP)
- Corresponding author
- Katoh, K.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-01-16
- Volume
- 30
- Issue
- 4
- Pages
- 772-780
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC3603318
- OpenAlex
- W2160378127
- Cited by
- 46,209
- References
- 49
- Citations by year
- 2026: 5174 · 2025: 5549 · 2024: 5538 · 2023: 4824 · 2022: 5005 · 2021: 5291 · 2020: 4177 · 2019: 3143 · 2018: 2383 · 2017: 1916 · 2016: 1503 · 2015: 981 · 2014: 574 · 2013: 112
- FWCI
- 473.96
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Molecular Biology and Evolution (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- National Institute of Advanced Industrial Science and Technology
- Ministry of Education, Culture, Sports, Science and Technology
- Agriculture and Agri-Food Canada
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- MAFFT, multiple sequence alignment, DNA sequence alignment, parallel computing, alignment errors, alignment software
- MeSH terms
- Algorithms, Amino Acid Sequence, Base Sequence, DNA, Fungal, DNA, Ribosomal, Fungi, Humans, Models, Genetic, Molecular Sequence Data, Phylogeny, Ribonucleases, RNA, Bacterial, Software, Transcription Factors, Sequence Alignment, Protein Structure, Tertiary, DNA, Ribosomal Spacer, Ribosome Subunits, Small, Bacterial, Quality Improvement
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