The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Parallelization of MAFFT for large-scale multiple sequence alignments
Open accessAbstract
Summary: We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers of sequences. The G-INS-1 option of MAFFT was recently reported to have higher accuracy than other methods for large data, but this method has been impractical for most large-scale analyses, due to the requirement of large computational resources. We introduce a scalable variant, G-large-INS-1, which has equivalent accuracy to G-INS-1 and is applicable to 50 000 or more sequences. Availability and implementation: This feature is available in MAFFT versions 7.355 or later at https://mafft.cbrc.jp/alignment/software/mpi.html. Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
Cited by
Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., et al. (2020) · The Lancet · doi:10.1016/s0140-6736(20)30251-8 · Cited by 11,907
Zhou, H., Ji, J., Chen, X., Bi, Y., Li, J., Wang, Q., Hu, T., Song, H., Zhao, R., Chen, Y., et al. (2021) · Cell · doi:10.1016/j.cell.2021.06.008 · Cited by 380
Levy Karin, E., Mirdita, M., & Söding, J. (2020) · Microbiome · doi:10.1186/s40168-020-00808-x · Cited by 299
“We aligned these sequences using MAFFT [44] and constructed the maximum-likelihood phylogeny using RAxML [45].”
MethodInfluentialThe structure, function and evolution of a complete human chromosome 8
Logsdon, G. A., Vollger, M. R., Hsieh, P., Mao, Y., Liskovykh, M. A., Koren, S., Nurk, S., Mercuri, L., Dishuck, P. C., Rhie, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03420-7 · Cited by 341
Tubiana, J., Schneidman-Duhovny, D., & Wolfson, H. J. (2022) · Nature Methods · doi:10.1038/s41592-022-01490-7 · Cited by 274
Metadata
- Authors
- Nakamura, T., Yamada, K. D., Tomii, K., & Katoh, K.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-03-01
- Volume
- 34
- Issue
- 14
- Pages
- 2490-2492
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2792034759
- Cited by
- 1,038
- References
- 1
- FWCI
- 27.07
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Nakamura, T., Yamada, K. D., Tomii, K., & Katoh, K. (2018). Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty121
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