The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
Open accessAbstract
Recombination is an important evolutionary force in bacteria, but it remains challenging to reconstruct the imports that occurred in the ancestry of a genomic sample. Here we present ClonalFrameML, which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction. ClonalFrameML can analyse hundreds of genomes in a matter of hours, and we demonstrate its usefulness on simulated and real datasets. We find evidence for recombination hotspots associated with mobile elements in Clostridium difficile ST6 and a previously undescribed 310kb chromosomal replacement in Staphylococcus aureus ST582. ClonalFrameML is freely available at http://clonalframeml.googlecode.com/.
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Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) · Systematic Biology · doi:10.1093/sysbio/syq010 · Cited by 18,376
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687
Lateral gene transfer and the nature of bacterial innovation
Ochman, H., Lawrence, J. G., & Groisman, E. A. (2000) · Nature · doi:10.1038/35012500 · Cited by 3,816
The Peopling of the Pacific from a Bacterial Perspective
Moodley, Y., Linz, B., Yamaoka, Y., Windsor, H. M., Breurec, S., Wu, J.-Y., Maady, A., Bernhöft, S., Thiberge, J.-M., Phuanukoonnon, S., et al. (2009) · Science · doi:10.1126/science.1166083 · Cited by 350
Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage
Golubchik, T., Batty, E. M., Miller, R. R., Farr, H., Young, B. C., Larner-Svensson, H., Fung, R., Godwin, H., Knox, K., Votintseva, A., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061319 · Cited by 212
Self-citationDingle, K. E., Didelot, X., Ansari, M. A., Eyre, D. W., Vaughan, A., Griffiths, D., Ip, C. L. C., Batty, E. M., Golubchik, T., Bowden, R., et al. (2013) · The Journal of Infectious Diseases · doi:10.1093/infdis/jis734 · Cited by 104
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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
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Arnold, B. J., Huang, I.-T., & Hanage, W. P. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00650-4 · Cited by 869
Walker, T. M., Kohl, T. A., Omar, S. V., Hedge, J., Del Ojo Elias, C., Bradley, P., Iqbal, Z., Feuerriegel, S., Niehaus, K. E., Wilson, D. J., et al. (2015) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(15)00062-6 · Cited by 638
Self-citationThe harmonic mean p -value for combining dependent tests
Wilson, D. J. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1814092116 · Cited by 449
Self-citationDingle, K. E., Didelot, X., Quan, T. P., Eyre, D. W., Stoesser, N., Golubchik, T., Harding, R. M., Wilson, D. J., Griffiths, D., Vaughan, A., et al. (2017) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(16)30514-x · Cited by 328
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Metadata
- Authors
- Didelot, X., & Wilson, D. J.
- Venue
- PLOS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2015-02-12
- Volume
- 11
- Issue
- 2
- Pages
- e1004041
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- OpenAlex
- W2025021478
- Cited by
- 882
- References
- 8
- FWCI
- 23.67
- Type
- journal article
- Language
- en
- Open access
- gold
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