The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm
Open accessAbstract
The evolution of homologous sequences affected by recombination or gene conversion cannot be adequately explained by a single phylogenetic tree. Many tree-based methods for sequence analysis, for example, those used for detecting sites evolving nonneutrally, have been shown to fail if such phylogenetic incongruity is ignored. However, it may be possible to propose several phylogenies that can correctly model the evolution of nonrecombinant fragments. We propose a model-based framework that uses a genetic algorithm to search a multiple-sequence alignment for putative recombination break points, quantifies the level of support for their locations, and identifies sequences or clades involved in putative recombination events. The software implementation can be run quickly and efficiently in a distributed computing environment, and various components of the methods can be chosen for computational expediency or statistical rigor. We evaluate the performance of the new method on simulated alignments and on an array of published benchmark data sets. Finally, we demonstrate that prescreening alignments with our method allows one to analyze recombinant sequences for positive selection.
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Cites
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
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“All four of these breakpoints were also identified with the tree-based recombination detection method GARD (Kosakovsky Pond et al., 2006).”
MethodWeaver, S., Shank, S. D., Spielman, S. J., Li, M., Muse, S. V., & Kosakovsky Pond, S. L. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msx335 · Cited by 983
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Temmam, S., Vongphayloth, K., Baquero, E., Munier, S., Bonomi, M., Regnault, B., Douangboubpha, B., Karami, Y., Chrétien, D., Sanamxay, D., et al. (2022) · Nature · doi:10.1038/s41586-022-04532-4 · Cited by 528
Identification of Wheat Gene Sr35 That Confers Resistance to Ug99 Stem Rust Race Group
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Identification of Rodent Homologs of Hepatitis C Virus and Pegiviruses
Kapoor, A., Simmonds, P., Scheel, T. K. H., Hjelle, B., Cullen, J. M., Burbelo, P. D., Chauhan, L. V., Duraisamy, R., Sanchez Leon, M., Jain, K., et al. (2013) · mBio · doi:10.1128/mbio.00216-13 · Cited by 256
Metadata
- Authors
- Kosakovsky Pond, S. L., Posada, D., Gravenor, M. B., Woelk, C. H., & Frost, S. D. W.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-07-03
- Volume
- 23
- Issue
- 10
- Pages
- 1891-1901
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2131203559
- Cited by
- 945
- References
- 5
- FWCI
- 12.16
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Kosakovsky Pond, S. L., Posada, D., Gravenor, M. B., Woelk, C. H., & Frost, S. D. W. (2006). Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msl051
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