MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Open accessAbstract
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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The positive selection analysis was conducted twice using different aligners (Muscle and Mafft).
“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
Because BLS alignments are very different from state-of-the-art software alignments, it is difficult to fairly compare them as alignments.
“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]
The three mutations in S1 (N501Y, A570D, ΔH69/V70) did not appear to impact neutralisation in a pseudovirus assay.
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617 · see citing works
The PyMOL Molecular Graphics System
DeLano, W. L. (2002) · Medical Entomology and Zoology · Cited by 18,147 · see citing works
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Katoh, K. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf436 · Cited by 17,027 · see citing works
Self-citationFast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
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 · see citing works
The Pfam Protein Families Database
Bateman, A. G. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.276 · Cited by 14,062 · see citing works
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. E., & Barton, G. J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp033 · Cited by 10,011 · see citing works
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 6,916 · see citing works
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 · see citing works
MAFFT version 5: improvement in accuracy of multiple sequence alignment
Katoh, K., Kuma, K., Toh, H., & Miyata, T. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki198 · Cited by 5,063 · see citing works
Self-citationThe Ribosomal Database Project: improved alignments and new tools for rRNA analysis
Cole, J., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A., Mcgarrell, D., Marsh, T., Garrity, G., et al. (2008) · Nucleic Acids Res. · doi:10.1093/nar/gkn879 · Cited by 4,940 · see citing works
The Pfam protein families database
Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1065 · Cited by 3,719 · see citing works
Recent developments in the MAFFT multiple sequence alignment program
Katoh, K., & Toh, H. (2008) · Briefings Bioinform. · doi:10.1093/bib/bbn013 · Cited by 3,707 · see citing works
Self-citationCLUSTAL: a package for performing multiple sequence alignment on a microcomputer
Higgins, D. G., & Sharp, P. M. (1988) · Gene · doi:10.1016/0378-1119(88)90330-7 · Cited by 3,394 · see citing works
Progressive sequence alignment as a prerequisitetto correct phylogenetic trees
Feng, D.-F., & Doolittle, R. F. (1987) · Journal of Molecular Evolution · doi:10.1007/bf02603120 · Cited by 1,883 · see citing works
Cannone, J. J., Subramanian, S., Schnare, M. N., Collett, J. R., D'Souza, L. M., Du, Y., Feng, B. Y., Lin, N., Madabusi, L. V., Müller, K. M., et al. (2002) · BMC Bioinformatics · doi:10.1186/1471-2105-3-2 · Cited by 1,614 · see citing works
Multiple Alignment of DNA Sequences with MAFFT
Katoh, K., Asimenos, G., & Toh, H. (2009) · Methods in molecular biology · doi:10.1007/978-1-59745-251-9_3 · Cited by 1,436 · see citing works
Self-citationPROMALS3D: a tool for multiple protein sequence and structure alignments
Pei, J., Kim, B., & Grishin, N. V. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn072 · Cited by 1,269 · see citing works
Adaptive seeds tame genomic sequence comparisonPreprint
Kiełbasa, S. M., Wan, R., Sato, K., Horton, P., & Frith, M. C. (2011) · Genome Research · doi:10.1101/gr.113985.110 · Cited by 1,252 · see citing works
Matsen, F. A., IV, Kodner, R. B., & Armbrust, E. V. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-538 · Cited by 1,026 · see citing works
Parallelization of the MAFFT multiple sequence alignment program
Katoh, K., & Toh, H. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq224 · Cited by 930 · see citing works
Self-citationPROSITE, a protein domain database for functional characterization and annotation
Sigrist, C. J. A., Cerutti, L., de Castro, E., Langendijk-Genevaux, P. S., Bulliard, V., Bairoch, A., & Hulo, N. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp885 · Cited by 852 · see citing works
Katoh, K., & Toh, H. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-212 · Cited by 606 · see citing works
Self-citationMAFFT: Iterative Refinement and Additional Methods
Katoh, K., & Standley, D. M. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-646-7_8 · Cited by 520 · see citing works
Self-citationA strategy for the rapid multiple alignment of protein sequences
Barton, G. J., & Sternberg, M. J. E. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90316-0 · Cited by 478 · see citing works
INDELible: A Flexible Simulator of Biological Sequence Evolution
Fletcher, W., & Yang, Z. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp098 · Cited by 416 · see citing works
3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments
O’Sullivan, Ó., Suhre, K., Abergel, C., Higgins, D. G., & Notredame, C. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.04.058 · Cited by 318 · see citing works
SEPP: SATé-Enabled Phylogenetic Placement
MIRARAB, S., NGUYEN, N., & WARNOW, T. (2011) · Biocomputing 2012 · doi:10.1142/9789814366496_0024 · Cited by 251 · see citing works
Adding unaligned sequences into an existing alignment using MAFFT and LAST
Katoh, K., & Frith, M. C. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts578 · Cited by 242 · see citing works
Self-citationCOFFEE: an objective function for multiple sequence alignments.
Notredame, C., Holm, L., & Higgins, D. G. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.5.407 · Cited by 231 · see citing works
Nilsson, R., Veldre, V., Hartmann, M., Unterseher, M., Amend, A., Bergsten, J., Kristiansson, E., Ryberg, M., Jumpponen, A., & Abarenkov, K. (2010) · Fungal ecology · doi:10.1016/j.funeco.2010.05.002 · Cited by 227 · see citing works
A mutation data matrix for transmembrane proteins
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1994) · FEBS Letters · doi:10.1016/0014-5793(94)80429-x · Cited by 206 · see citing works
Aligning short reads to reference alignments and trees
Berger, S., & Stamatakis, A. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr320 · Cited by 191 · see citing works
The accuracy of several multiple sequence alignment programs for proteins
Nuin, P. A. S., Wang, Z., & Tillier, E. R. M. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-471 · Cited by 169 · see citing works
Phylogenetic assessment of alignments reveals neglected tree signal in gaps
Dessimoz, C., & Gil, M. (2010) · Genome biology · doi:10.1186/gb-2010-11-4-r37 · Cited by 132 · see citing works
Optimal alignment between groups of sequences and its application to multiple sequence alignment
Gotoh, O. (1993) · Computer applications in the biosciences · doi:10.1093/bioinformatics/9.3.361 · Cited by 127 · see citing works
Mind the Gaps: Evidence of Bias in Estimates of Multiple Sequence Alignments
Golubchik, T., Wise, M. J., Easteal, S., & Jermiin, L. S. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm176 · Cited by 124 · see citing works
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm
Löytynoja, A., Vilella, A. J., & Goldman, N. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts198 · Cited by 123 · see citing works
A fast structural multiple alignment method for long RNA sequences
Tabei, Y., Kiryu, H., Taishin Kin, A., & Asai, K. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-33 · Cited by 117 · see citing works
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences
Katoh, K., & Toh, H. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl592 · Cited by 106 · see citing works
Self-citationA novel randomized iterative strategy for aligning multiple protein sequences
Berger, M. P., & Munson, P. J. (1991) · Computer applications in the biosciences · doi:10.1093/bioinformatics/7.4.479 · Cited by 100 · see citing works
Class of Multiple Sequence Alignment Algorithm Affects Genomic Analysis
Blackburne, B. P., & Whelan, S. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss256 · Cited by 76 · see citing works
Measuring the distance between multiple sequence alignments
Blackburne, B. P., & Whelan, S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr701 · Cited by 75 · see citing works
Rick, S. W., Erickson, J. W., & Burt, S. K. (1998) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19980701)32:1 · Cited by 66 · see citing works
A weighting system and aigorithm for aligning many phylogenetically related sequences
Gotoh, O. (1995) · Computer applications in the biosciences · doi:10.1093/bioinformatics/11.5.543 · Cited by 65 · see citing works
Letsch, H. O., Kück, P., Stocsits, R. R., & Misof, B. Y. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq140 · Cited by 53 · see citing works
ASH structure alignment package: Sensitivity and selectivity in domain classification
Standley, D. M., Toh, H., & Nakamura, H. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-116 · Cited by 45 · see citing works
Self-citationDetecting local structural similarity in proteins by maximizing number of equivalent residues
Standley, D. M., Toh, H., & Nakamura, H. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20211 · Cited by 23 · see citing works
Self-citationPicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach
Sahraeian, S. M. E., & Yoon, B.-J. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-s1-s38 · Cited by 17 · see citing works
PhyLAT: a phylogenetic local alignment tool
Sun, H., & Buhler, J. D. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts158 · Cited by 7 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
A new coronavirus associated with human respiratory disease in China
Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., et al. (2020) · Nature · doi:10.1038/s41586-020-2008-3 · Cited by 11,688 · see citing works
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
Katoh, K., Rozewicki, J., & Yamada, K. D. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbx108 · Cited by 8,909 · see citing works
Self-citationOrthoFinder: phylogenetic orthology inference for comparative genomics
Emms, D. M., & Kelly, S. (2019) · Genome Biology · doi:10.1186/s13059-019-1832-y · Cited by 7,676 · see citing works
Deciphering key features in protein structures with the new ENDscript server
Robert, X., & Gouet, P. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku316 · Cited by 7,053 · see citing works
Accurate prediction of protein structures and interactions using a 3-track network
Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · doi:10.1101/2021.06.14.448402 · Cited by 5,542 · see citing works
Comparative Protein Structure Modeling Using MODELLER
Webb, B., & Šali, A. (2016) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.3 · Cited by 4,349 · see citing works
The EMBL-EBI search and sequence analysis tools APIs in 2019
Madeira, F., Park, Y. M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., Basutkar, P., Tivey, A. R. N., Potter, S. C., Finn, R. D., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz268 · Cited by 4,167 · see citing works
Zhang, D., Gao, F., Jakovlić, I., Jakovlić, I., Zou, H., Zhang, J., & Wang, G. (2019) · Molecular Ecology Resources · doi:10.1111/1755-0998.13096 · Cited by 4,122 · see citing works
Ashkenazy, H., Abadi, S., Martz, E., Chay, O., Mayrose, I., Pupko, T., & Ben-Tal, N. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw408 · Cited by 3,163 · see citing works
Emms, D. M., & Kelly, S. (2015) · Genome Biology · doi:10.1186/s13059-015-0721-2 · Cited by 3,408 · see citing works
The complete sequence of a human genome
Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., et al. (2022) · Science · doi:10.1126/science.abj6987 · Cited by 3,136 · see citing works
Zheng, J., Wittouck, S., Salvetti, E., Franz, C. M. A. P., Harris, H. M. B., Mattarelli, P., O’Toole, P. W., Pot, B., Vandamme, P., Walter, J., et al. (2020) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijsem.0.004107 · Cited by 3,313 · see citing works
High expression of ACE2 receptor of 2019-nCoV on the epithelial cells of oral mucosa
Xu, H., Zhong, L., Deng, J., Peng, J., Dan, H., Zeng, X., Li, T., & Chen, Q. (2020) · International Journal of Oral Science · doi:10.1038/s41368-020-0074-x · Cited by 2,838 · see citing works
Phylogenomics resolves the timing and pattern of insect evolution
Misof, B., Liu, S., Meusemann, K., Peters, R. S., Donath, A., Mayer, C., Frandsen, P. B., Ware, J., Flouri, T., Beutel, R. G., et al. (2014) · Science · doi:10.1126/science.1257570 · Cited by 2,694 · see citing works
A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core
Zimmermann, L., Stephens, A., Nam, S.-Z., Rau, D., Kübler, J., Lozajic, M., Gabler, F., Söding, J., Lupas, A. N., & Alva, V. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.12.007 · Cited by 2,522 · see citing works
Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303 · see citing works
Starr, T. N., Greaney, A. J., Hilton, S. K., Ellis, D., Crawford, K. H. D., Dingens, A. S., Navarro, M. J., Bowen, J. E., Tortorici, M. A., Walls, A. C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.08.012 · Cited by 1,956 · see citing works
BUSCO applications from quality assessments to gene prediction and phylogenomics
Waterhouse, R. M., Seppey, M., Simão, F. A., Manni, M., Ioannidis, P., Klioutchnikov, G., Kriventseva, E. V., & Zdobnov, E. M. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx319 · Cited by 2,214 · see citing works
Huerta‐Cepas, J., Szklarczyk, D., Forslund, S. K., Cook, H., Heller, D., Walter, M. C., Rattei, T., Mende, D. R., Sunagawa, S., Kuhn, M., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1248 · Cited by 2,062 · see citing works
Allio, R., Schomaker-Bastos, A., Romiguier, J., Prosdocimi, F., Nabholz, B., & Delsuc, F. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13160 · Cited by 1,921 · see citing works
Detection of a SARS-CoV-2 variant of concern in South Africa
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2021) · Nature · doi:10.1038/s41586-021-03402-9 · Cited by 2,510 · see citing works
Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., Beghini, F., Manghi, P., Tett, A., Ghensi, P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.001 · Cited by 1,591 · see citing works
CheckV assesses the quality and completeness of metagenome-assembled viral genomes
Nayfach, S., Camargo, A. P., Schulz, F., Eloe‐Fadrosh, E. A., Roux, S., & Kyrpides, N. C. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-00774-7 · Cited by 1,779 · see citing works
SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation
Muhire, B. M., Varsani, A., & Martin, D. P. (2014) · PLoS ONE · doi:10.1371/journal.pone.0108277 · Cited by 1,774 · see citing works
The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024
Madeira, F., Madhusoodanan, N., Lee, J., Eusebi, A., Niewielska, A., Tivey, A., Lopez, R., & Butcher, S. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae241 · Cited by 1,666 · see citing works
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., & Lemmon, A. R. (2015) · Nature · doi:10.1038/nature15697 · Cited by 1,668 · see citing works
Redefining the invertebrate RNA virosphere
Shī, M., Lin, X., Tian, J.-H., Chen, L., Chen, X., Li, C., Qin, X.-C., Li, J., Cao, J., Eden, J., et al. (2016) · Nature · doi:10.1038/nature20167 · Cited by 1,649 · see citing works
Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil
Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D. D. S., Mishra, S., Crispim, M. A. E., Sales, F. C. S., Hawryluk, I., McCrone, J. T., et al. (2021) · Science · doi:10.1126/science.abh2644 · Cited by 1,461 · see citing works
Blanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., Manghi, P., Dubois, L., Huang, K. D., Thomas, A. M., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01688-w · Cited by 1,442 · see citing works
Shukla, S., Mishra, B., Avashthi, H., & Chandra, M. (2021) · Elsevier eBooks · doi:10.1016/b978-0-323-89775-4.00003-1 · Cited by 1,513 · see citing works
Dabney, J., Knapp, M., Glocke, I., Gansauge, M.-T., Weihmann, A., Nickel, B., Valdiosera, C., García, N., Pääbo, S., Arsuaga, J.-L., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1314445110 · Cited by 1,443 · see citing works
SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion
Mlcochova, P., Kemp, S. A., Dhar, M. S., Papa, G., Meng, B., Ferreira, I. A. T. M., Datir, R., Collier, D. A., Albecka, A., Singh, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03944-y · Cited by 1,337 · see citing works
SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
Page, A. J., Taylor, B. E. W., Delaney, A. J., Soares, J., Seemann, T., Keane, J. A., & Harris, S. R. (2016) · Microbial Genomics · doi:10.1099/mgen.0.000056 · Cited by 1,395 · see citing works
UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction
Na, S.-I., Kim, Y. O., Yoon, S.-H., Ha, S. M., Baek, I., & Chun, J. (2018) · The Journal of Microbiology · doi:10.1007/s12275-018-8014-6 · Cited by 1,380 · see citing works
Asgard archaea illuminate the origin of eukaryotic cellular complexity
Zaremba-Niedzwiedzka, K., Caceres, E. F., Saw, J. H., Bäckström, D., Juzokaite, L., Vancaester, E., Seitz, K. W., Anantharaman, K., Starnawski, P., Kjeldsen, K. U., et al. (2017) · Nature · doi:10.1038/nature21031 · Cited by 1,226 · see citing works
Greaney, A. J., Loes, A. N., Crawford, K. H. D., Starr, T. N., Malone, K. D., Chu, H. Y., & Bloom, J. D. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.02.003 · Cited by 1,178 · see citing works
Complex archaea that bridge the gap between prokaryotes and eukaryotes
Spang, A., Saw, J. H., Jørgensen, S. L., Zaremba-Niedzwiedzka, K., Martijn, J., Lind, A. E., van Eijk, R., Schleper, C., Guy, L., & Ettema, T. J. G. (2015) · Nature · doi:10.1038/nature14447 · Cited by 1,324 · see citing works
L1 drives IFN in senescent cells and promotes age-associated inflammation
De Cecco, M., Ito, T., Petrashen, A. P., Elias, A. E., Skvir, N. J., Criscione, S. W., Caligiana, A., Brocculi, G., Adney, E. M., Boeke, J. D., et al. (2019) · Nature · doi:10.1038/s41586-018-0784-9 · Cited by 1,255 · see citing works
“Multiple sequence alignments were calculated using MAFFT (Multiple Alignment using Fast Fourier Transform) with the L-INS-i algorithm (accurate for alignments of 200 sequences) 57 .”
BUSCO: Assessing Genomic Data Quality and Beyond
Manni, M., Berkeley, M., Seppey, M., & Zdobnov, E. M. (2021) · Current Protocols · doi:10.1002/cpz1.323 · Cited by 1,303 · see citing works
Olson, R., Assaf, R., Brettin, T. S., Conrad, N. R., Cucinell, C. A., Davis, J. J., Dempsey, D. M., Dickerman, A., Dietrich, E. M., Kenyon, R. W., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1003 · Cited by 1,271 · see citing works
Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors
Konermann, S., Lotfy, P., Brideau, N. J., Oki, J., Shokhirev, M. N., & Hsu, P. D. (2018) · Cell · doi:10.1016/j.cell.2018.02.033 · Cited by 1,164 · see citing works
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems
Shmakov, S., Abudayyeh, O. O., Makarova, K. S., Wolf, Y. I., Gootenberg, J. S., Semenova, E., Станиславович, М. Л., Joung, J., Konermann, S., Severinov, K., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.10.008 · Cited by 1,221 · see citing works
Edgar, R. C. (2022) · Nature Communications · doi:10.1038/s41467-022-34630-w · Cited by 1,217 · see citing works
Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection
East-Seletsky, A., O’Connell, M. R., Knight, S. C., Burstein, D. E., Cate, J. H. D., Tjian, R., & Doudna, J. A. (2016) · Nature · doi:10.1038/nature19802 · Cited by 1,180 · see citing works
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2020) · doi:10.1101/2020.12.21.20248640 · Cited by 2,535 · see citing works
“It performs alignment of genotypes in MAFFT 19 , phylogenetic tree inference in IQ-Tree 20 , tree dating and ancestral state construction and annotation (https://github.com/nextstrain/ncov).”
Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants
Qiao, X., Li, Q., Yin, H., Qi, K., Li, L., Wang, R., Zhang, S., & Paterson, A. H. (2019) · Genome biology · doi:10.1186/s13059-019-1650-2 · Cited by 1,180 · see citing works
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
Meng, G., Li, Y., Yang, C., & Liu, S. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz173 · Cited by 1,162 · see citing works
Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity
Meng, B., Abdullahi, A., Ferreira, I. A. T. M., Goonawardane, N., Saito, A., Kimura, I., Yamasoba, D., Gerber, P. P., Fatihi, S., Rathore, S., et al. (2022) · Nature · doi:10.1038/s41586-022-04474-x · Cited by 1,146 · see citing works
Comparative Protein Structure Modeling Using MODELLER
Webb, B., & Šali, A. (2014) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0506s47 · Cited by 1,141 · see citing works
Thomas, A. M., Manghi, P., Asnicar, F., Pasolli, E., Armanini, F., Zolfo, M., Beghini, F., Manara, S., Karcher, N., Pozzi, C., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0405-7 · Cited by 1,030 · see citing works
Ahmed, S. F., Quadeer, A. A., & McKay, M. R. (2020) · Viruses · doi:10.3390/v12030254 · Cited by 1,116 · see citing works
Byrska-Bishop, M., Evani, U. S., Zhao, X., Basile, A. O., Abel, H. J., Regier, A. A., Corvelo, A., Clarke, W. E., Musunuri, R., Nagulapalli, K., et al. (2022) · Cell · doi:10.1016/j.cell.2022.08.004 · Cited by 1,094 · see citing works
Azani, N., Babineau, M., Bailey, C. D., Banks, H. I., Barbosa, A. R., Pinto, R. B., Boatwright, J. S., Borges, L. M., Brown, G. K., Bruneau, A., et al. (2017) · Taxon · doi:10.12705/661.3 · Cited by 1,098 · see citing works
SARS-CoV-2 evolution during treatment of chronic infection
Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., Hosmillo, M., Rees-Spear, C., Mlcochova, P., Lumb, I. U., et al. (2021) · Nature · doi:10.1038/s41586-021-03291-y · Cited by 1,097 · see citing works
Constructing a broadly inclusive seed plant phylogeny
Smith, S. A., & Brown, J. W. (2018) · American Journal of Botany · doi:10.1002/ajb2.1019 · Cited by 1,085 · see citing works
Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift
Cameroni, E., Bowen, J. E., Rosen, L. E., Saliba, C., Zepeda, S. K., Culap, K., Pinto, D., VanBlargan, L. A., Marco, A. D., di Iulio, J., et al. (2021) · Nature · doi:10.1038/s41586-021-04386-2 · Cited by 1,043 · see citing works
Nextclade: clade assignment, mutation calling and quality control for viral genomes
Aksamentov, I., Roemer, C., Hodcroft, E. B., & Neher, R. A. (2021) · The Journal of Open Source Software · doi:10.21105/joss.03773 · Cited by 1,061 · see citing works
The Atlantic salmon genome provides insights into rediploidization
Lien, S., Koop, B. F., Sandve, S. R., Miller, J. R., Kent, M., Nome, T., Hvidsten, T. R., Leong, J. S., Minkley, D. R., Zimin, A. V., et al. (2016) · Nature · doi:10.1038/nature17164 · Cited by 1,043 · see citing works
The physiology and habitat of the last universal common ancestor
Weiss, M. C., Sousa, F. L., Mrnjavac, N., Neukirchen, S., Roettger, M., Nelson-Sathi, S., & Martin, W. F. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.116 · Cited by 1,049 · see citing works
PHYLUCE is a software package for the analysis of conserved genomic loci
Faircloth, B. C. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv646 · Cited by 1,019 · see citing works
Kapli, P., Lutteropp, S., Zhang, J., Kobert, K., Pavlidis, P., Stamatakis, A., & Flouri, T. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx025 · Cited by 1,046 · see citing works
Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer
Dominguez-Bello, M. G., De Jesus-Laboy, K. M., Shen, N., Cox, L. M., Amir, A., Gonzalez, A., Bokulich, N. A., Song, S. J., Hoashi, M., Rivera-Vinas, J. I., et al. (2016) · Nature Medicine · doi:10.1038/nm.4039 · Cited by 1,014 · see citing works
A computational framework to explore large-scale biosynthetic diversity
Navarro-Muñoz, J. C., Mojica, N. S., Mullowney, M. W., Kautsar, S. A., Tryon, J. H., Parkinson, E. I., Santos, E. L. C. D. L., Yeong, M., Cruz‐Morales, P., Abubucker, S., et al. (2019) · Nature Chemical Biology · doi:10.1038/s41589-019-0400-9 · Cited by 1,032 · see citing works
The EMBL-EBI bioinformatics web and programmatic tools framework
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 1,028 · see citing works
Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
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 · see citing works
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 · see citing works
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 989 · see citing works
Kuraku, S., Zmasek, C. M., Nishimura, O., & Katoh, K. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt389 · Cited by 975 · see citing works
Self-citationImproving 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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 900 · see citing works
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 893 · see citing works
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 860 · see citing works
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 847 · see citing works
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 · see citing works
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 · see citing works
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 830 · see citing works
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 841 · see citing works
Sela, I., Ashkenazy, H., Katoh, K., & Pupko, T. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv318 · Cited by 835 · see citing works
Self-citationNeglecting 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 · see citing works
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 · see citing works
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 818 · see citing works
Self-citationMassively 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 · see citing works
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 · see citing works
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 785 · see citing works
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 · see citing works
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 · see citing works
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 775 · see citing works
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 · see citing works
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 753 · see citing works
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 · see citing works
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 · see citing works
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 751 · see citing works
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 · see citing works
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 716 · see citing works
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 · see citing works
- 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 · 2012: 2
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
