Cited by 46,209Genomics and Phylogenetic StudiesFractal and DNA sequence analysisRNA and protein synthesis mechanisms

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

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Katoh, K., Standley, D. M.·2013·Molecular Biology and Evolution

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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.

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Fig. 1. Assumptions on the phylogenetic relationship in different options of MAFFT. (A) mafft-profile, (B) ––addprofile, (C), misuse of mafft-profile, and (D) ––add or ––addprofile.CC BY-NC · PubMed Central

Fig. 2. ITS alignments by different options of MAFFT, displayed on Jalview (Waterhouse et al. 2009). (A, B) Incorrect alignments by the FFT-NS-2 and L-INS-i algorithms, respectively. (C) An incorrect alignment by mafft-profile. The full-length sequences were aligned with the L-INS-i algorithm and then each new sequence was separately added to the full-length alignment, using mafft-profile. (D) Reasonable alignment by a two-step strategy. The ––6merpair ––addfragments option was used at the second step. (E) Reordered version of D; sequences are ordered such that similar sequences are placed closely. All calculations were performed using 16 cores on a Linux PC with 2.67 GHz Intel Xeon E7-8837/256 GB RAM.CC BY-NC · PubMed Central

Fig. 3. (A) A part of output of the ––treeout option showing the phylogenetic positions of new sequences (new#) in the tree of the existing alignment (backbone#), estimated before the alignment calculation. This file also shows a Newick format tree of the existing alignment (not shown in this figure). For each new sequence, the nearest sequence in the existing alignment (nearest sequence), approximate distance to the nearest sequence (approximate distance), and the members of the sister group (sister group) are shown. (B) Graphical representation of (A).CC BY-NC · PubMed Central

Fig. 4. (A) Superposition of 3v33, 2qip, and 1taq structures visualized by PyMOL (Schrödinger LLC 2010). (B) MAFFT-L-INS-i sequence alignment displayed on jalview (Waterhouse et al. 2009). Misaligned Ds are highlighed in red. (C) Structure-informed MSA with correctly aligned Ds; Alpha helices and beta sheets are shown in blue and yellow, respectively, in (A–C).CC BY-NC · PubMed Central

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Sievers, F., Wilm, A., Dineen, D., Gibson, T., Karplus, K., Li, W.-Z., Lopez, R., McWilliam, H., Remmert, M., Söding, J., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.75 · Cited by 15,576
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The rapid generation of mutation data matrices from protein sequences
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992) · Computer applications in the biosciences · doi:10.1093/bioinformatics/8.3.275 · Cited by 7,003
Amino acid substitution matrices from protein blocks.
Henikoff, S., & Henikoff, J. G. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.22.10915 · Cited by 6,218
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Show all 49 references

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Li, W., Cowley, A., Uludağ, M., Gür, T., McWilliam, H., Squizzato, S., Park, Y. M., Buso, N., & López, R. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv279 · Cited by 1,036
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Yurkovetskiy, L., Wang, X., Pascal, K. E., Tomkins-Tinch, C., Nyalile, T. P., Wang, Y., Baum, A., Diehl, W. E., Dauphin, A., Carbone, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.032 · Cited by 1,025
Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition
Greaney, A. J., Starr, T. N., Gilchuk, P., Zost, S. J., Binshtein, E., Loes, A. N., Hilton, S. K., Huddleston, J., Eguia, R., Crawford, K. H. D., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2020.11.007 · Cited by 1,016
“All 94,233 spike sequences on GISAID as of 6 September 2020 were downloaded and aligned via mafft (Katoh and Standley, 2013).”
The Transporter Classification Database (TCDB): recent advances
Saier, M. H., Reddy, V. S., Tsu, B. V., Ahmed, M. S., Li, C., & Moreno‐Hagelsieb, G. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1103 · Cited by 1,010
RESCRIPt: Reproducible sequence taxonomy reference database management
(2021) · doi:10.1371/journal.pcbi.1009581 · Cited by 983
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity
Kuraku, S., Zmasek, C. M., Nishimura, O., & Katoh, K. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt389 · Cited by 975
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Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction
Koblan, L. W., Doman, J. L., Wilson, C., Levy, J. M., Tay, T., Newby, G. A., Maianti, J. P., Raguram, A., & Liu, D. R. (2018) · Nature Biotechnology · doi:10.1038/nbt.4172 · Cited by 944
Cross‐species transmission of the newly identified coronavirus 2019‐nCoV
Ji, W., Wang, W., Zhao, X., Zai, J., & Li, X. (2020) · Journal of Medical Virology · doi:10.1002/jmv.25682 · Cited by 942
Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies
Barnes, C. O., West, A. P., Huey-Tubman, K. E., Hoffmann, M. A. G., Sharaf, N. G., Hoffman, P. R., Koranda, N., Gristick, H. B., Gaebler, C., Muecksch, F., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.025 · Cited by 795
Simulating 500 million years of evolution with a language model
Hayes, T., Rao, R., Akin, H., Sofroniew, N. J., Oktay, D., Lin, Z., Verkuil, R., Tran, V. Q., Deaton, J., Wiggert, M., et al. (2025) · Science · doi:10.1126/science.ads0018 · Cited by 937
The fossilized birth-death process for coherent calibration of divergence-time estimates
Heath, T. A., Huelsenbeck, J. P., & Stadler, T. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319091111 · Cited by 834
NGPhylogeny.fr: new generation phylogenetic services for non-specialists
Lemoine, F., Correia, D., Lefort, V., Doppelt‐Azeroual, O., Mareuil, F., Cohen‐Boulakia, S., & Gascuel, O. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz303 · Cited by 951
Evolutionary History of the Hymenoptera
Peters, R. S., Krogmann, L., Mayer, C., Donath, A., Gunkel, S., Meusemann, K., Kozlov, A. M., Podsiadłowski, L., Petersen, M., Lanfear, R., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.01.027 · Cited by 916
Viral and host factors related to the clinical outcome of COVID-19
Zhang, X., Tan, Y., Ling, Y., Lü, G., Liu, F., Yi, Z., Jia, X., Wu, M., Shi, B., Xu, S., et al. (2020) · Nature · doi:10.1038/s41586-020-2355-0 · Cited by 874
A genomic catalog of Earth’s microbiomes
Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N. J., Schulz, F., Wu, D., Páez-Espino, D., Chen, I.-M. A., Huntemann, M., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0718-6 · Cited by 890
Prospective mapping of viral mutations that escape antibodies used to treat COVID-19
Starr, T. N., Greaney, A. J., Addetia, A., Hannon, W. W., Choudhary, M. C., Dingens, A. S., Li, J. Z., & Bloom, J. D. (2021) · Science · doi:10.1126/science.abf9302 · Cited by 743
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
Asnicar, F., Thomas, A. M., Beghini, F., Mengoni, C., Manara, S., Manghi, P., Zhu, Q., Bolzan, M., Cumbo, F., May, U., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16366-7 · Cited by 869
HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment
Johnson, M. G., Gardner, E. M., Liu, Y., Medina, R., Goffinet, B., Shaw, A. J., Zerega, N. J. C., & Wickett, N. J. (2016) · Applications in Plant Sciences · doi:10.3732/apps.1600016 · Cited by 845
The Tree of Life and a New Classification of Bony Fishes
Betancur‐R, R., Broughton, R. E., WILEY, E. O., Carpenter, K. E., Lopez, J. A., Li, C., Holcroft, N. I., Arcila, D., Sanciangco, M. D. A., Cureton, J. C., et al. (2013) · PLoS Currents · doi:10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288 · Cited by 871
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters
Sela, I., Ashkenazy, H., Katoh, K., & Pupko, T. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv318 · Cited by 835
Self-citation
Neglecting legumes has compromised human health and sustainable food production
Foyer, C. H., Lam, H., Nguyen, H. T., Siddique, K. H. M., Varshney, R. K., Colmer, T. D., Cowling, W. A., Bramley, H., Mori, T. A., Hodgson, J. M., et al. (2016) · Nature Plants · doi:10.1038/nplants.2016.112 · Cited by 822
Coronavirus Disease 2019 (COVID-19) Re-infection by a Phylogenetically Distinct Severe Acute Respiratory Syndrome Coronavirus 2 Strain Confirmed by Whole Genome Sequencing
To, K. K.-W., Hung, I. F.-N., Ip, J. D., Chu, A. W.-H., Chan, W.-M., Tam, A. R., Fong, C. H.-Y., Yuan, S., Tsoi, H.-W., Ng, A. C.-K., et al. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa1275 · Cited by 746
MAFFT-DASH: integrated protein sequence and structural alignment
Rozewicki, J., Li, S., Amada, K. M., Standley, D. M., & Katoh, K. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz342 · Cited by 835
Self-citation
Massively multiplexed nucleic acid detection with Cas13
Ackerman, C. M., Myhrvold, C., Thakku, S. G., Freije, C. A., Metsky, H. C., Yang, D. K., Ye, S. H., Boehm, C. K., Kosoko-Thoroddsen, T.-S. F., Kehe, J., et al. (2020) · Nature · doi:10.1038/s41586-020-2279-8 · Cited by 813
Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism
Davison, J., Moora, M., Öpik, M., Adholeya, A., Ainsaar, L., Bâ, A., Burla, S., Diédhiou, A. G., Hiiesalu, I., Jairus, T., et al. (2015) · Science · doi:10.1126/science.aab1161 · Cited by 808
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics
Evans, P. N., Parks, D. H., Chadwick, G. L., Robbins, S. J., Orphan, V. J., Golding, S. D., & Tyson, G. W. (2015) · Science · doi:10.1126/science.aac7745 · Cited by 804
Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses
Li, C., Shī, M., Tian, J.-H., Lin, X., Kang, Y., Chen, L., Qin, X.-C., Xu, J., Holmes, E. C., & Zhang, Y. (2015) · eLife · doi:10.7554/elife.05378 · Cited by 788
The evolutionary history of vertebrate RNA viruses
Shī, M., Lin, X., Chen, X., Tian, J.-H., Chen, L., Li, K., Wang, W., Eden, J., Shen, J., Liu, L., et al. (2018) · Nature · doi:10.1038/s41586-018-0012-7 · Cited by 763
Emergence of genomic diversity and recurrent mutations in SARS-CoV-2
van Dorp, L., Acman, M., Richard, D., Shaw, L. P., Ford, C. E., Ormond, L., Owen, C. J., Pang, J., Tan, C. C. S., Boshier, F. A. T., et al. (2020) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2020.104351 · Cited by 780
Long-term benefit of microbiota transfer therapy on autism symptoms and gut microbiota
Kang, D.-W., Adams, J. B., Coleman, D. M., Pollard, E. L., Maldonado, J., McDonough-Means, S., Caporaso, J. G., & Krajmalnik-Brown, R. (2019) · Scientific Reports · doi:10.1038/s41598-019-42183-0 · Cited by 749
Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event
Paraskevis, D. N., Kostaki, E. G., Magiorkinis, G., Panayiotakopoulos, G., Sourvinos, G., & Tsiodras, S. (2020) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2020.104212 · Cited by 769
Genomic evidence for reinfection with SARS-CoV-2: a case study
Tillett, R. L., Sevinsky, J. R., Hartley, P. D., Kerwin, H., Crawford, N. F., Gorzalski, A. J., Laverdure, C., Verma, S. C., Rossetto, C. C., Jackson, D. K., et al. (2020) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(20)30764-7 · Cited by 755
Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa
Ariyawansa, H. A., Hyde, K. D., Jayasiri, S. C., Buyck, B., Chethana, K. W. T., Dai, D. Q., Dai, Y. C., Daranagama, D. A., Jayawardena, R. S., Lücking, R., et al. (2015) · Fungal Diversity · doi:10.1007/s13225-015-0346-5 · Cited by 751
WormBase ParaSite − a comprehensive resource for helminth genomics
Howe, K., Bolt, B. J., Shafie, M., Kersey, P. J., & Berriman, M. (2016) · Molecular and Biochemical Parasitology · doi:10.1016/j.molbiopara.2016.11.005 · Cited by 718
A Novel Coronavirus Genome Identified in a Cluster of Pneumonia Cases — Wuhan, China 2019−2020
Tan, W., Zhao, X., Ma, X., Wang, W., Niu, P., Xu, W., Gao, G. F., & Wu, G. (2020) · China CDC Weekly · doi:10.46234/ccdcw2020.017 · Cited by 741
Estimating infectiousness throughout SARS-CoV-2 infection course
Jones, T. C., Biele, G., Mühlemann, B., Veith, T., Schneider, J. A., Beheim-Schwarzbach, J., Bleicker, T., Tesch, J., Schmidt, M. L., Sander, L. E., et al. (2021) · Science · doi:10.1126/science.abi5273 · Cited by 752
SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R., Walls, A. C., Kemp S, S. A., Bassi, J., Pinto, D., Fregni, C. S., et al. (2021) · doi:10.1101/2021.01.19.21249840 · Cited by 729

Authors: Katoh, K., & Standley, D. M.
Affiliations: Immunology Frontier Research Center, The University of Osaka (JP)
Corresponding author: Katoh, K.
ORCID: Katoh, K.
Standley, D. M.
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
DOI: 10.1093/molbev/mst010
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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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

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