The DOI matches its Crossref record; 58 of the 58 references it cites were found in a registry or an index.
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Open accessAbstract
The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. These datasets, of increasing size, often include examples of multiple different mechanisms of horizontal sequence transfer resulting in substantial alterations to prokaryotic chromosomes. The impact of these processes demands rapid and flexible approaches able to account for recombination when reconstructing isolates’ recent diversification. Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistically parameterized models of bacterial evolution, and achieves convergence in only a few hours on alignments of hundreds of bacterial genome sequences. Gubbins is appropriate for reconstructing the recent evolutionary history of a variety of haploid genotype alignments, as it makes no assumptions about the underlying mechanism of recombination. The software is freely available for download at github.com/sanger-pathogens/Gubbins, implemented in Python and C and supported on Linux and Mac OS X.
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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
Kulldorff, M. (1997) · Communications in Statistics - Theory and Methods · doi:10.1080/03610929708831995 · Cited by 3,939
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
Darling, A. E., Mau, B., & Perna, N. T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011147 · Cited by 3,848
Comparison of phylogenetic trees
Robinson, D. F., & Foulds, L. R. (1981) · Mathematical Biosciences · doi:10.1016/0025-5564(81)90043-2 · Cited by 2,701
Smith, J. M., Smith, N. H., O'Rourke, M., & Spratt, B. G. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.10.4384 · Cited by 1,802
Analyzing the mosaic structure of genes
Smith, J. (1992) · Journal of Molecular Evolution · doi:10.1007/bf00182389 · Cited by 1,625
RDP3: a flexible and fast computer program for analyzing recombination
Martin, D. P., Lemey, P., Lott, M., Moulton, V., Posada, D., & Lefeuvre, P. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq467 · Cited by 1,613
A Simple and Robust Statistical Test for Detecting the Presence of Recombination
Bruen, T. C., Philippe, H., & Bryant, D. (2006) · Genetics · doi:10.1534/genetics.105.048975 · Cited by 1,382
Evolution of MRSA During Hospital Transmission and Intercontinental Spread
Harris, S. R., Feil, E. J., Holden, M. T. G., Quail, M. A., Nickerson, E. K., Chantratita, N., Gardete, S., Tavares, A., Day, N., Lindsay, J. A., et al. (2010) · Science · doi:10.1126/science.1182395 · Cited by 1,091
Self-citationRapid Pneumococcal Evolution in Response to Clinical Interventions
Croucher, N. J., Harris, S. R., Fraser, C., Quail, M. A., Burton, J., van der Linden, M., McGee, L., von Gottberg, A., Song, J. H., Ko, K. S., et al. (2011) · Science · doi:10.1126/science.1198545 · Cited by 886
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Horizontal gene transfer and adaptive evolution in bacteria.
Arnold, B. J., Huang, I.-T., & Hanage, W. P. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00650-4 · Cited by 869
Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread
David, S., Reuter, S., Harris, S. R., Glasner, C., Feltwell, T., Argimon, S., Abudahab, K., Goater, R., Giani, T., Errico, G., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0492-8 · Cited by 773
Self-citationWhole genome-based population biology and epidemiological surveillance of Listeria monocytogenes
Moura, A., Criscuolo, A., Pouseele, H., Maury, M. M., Leclercq, A., Tarr, C., Björkman, J. T., Dallman, T., Reimer, A., Enouf, V., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.185 · Cited by 668
Phandango: an interactive viewer for bacterial population genomics
Hadfield, J., Croucher, N. J., Goater, R. J., Abudahab, K., Aanensen, D. M., & Harris, S. R. (2018) · Bioinformatics · doi:10.1093/bioinformatics/btx610 · Cited by 659
Self-citationEmergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium
Bryant, J. M., Grogono, D. M., Rodriguez-Rincon, D., Everall, I., Brown, K. P., Moreno, P., Verma, D., Hill, E., Drijkoningen, J., Gilligan, P., et al. (2016) · Science · doi:10.1126/science.aaf8156 · Cited by 587
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Metadata
- Authors
- Croucher, N. J., Page, A. J., Connor, T. R., Delaney, A. J., Keane, J. A., Bentley, S. D., Parkhill, J., & Harris, S. R.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-11-20
- Volume
- 43
- Issue
- 3
- Pages
- e15-e15
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W1972145956
- Cited by
- 2,741
- References
- 58
- FWCI
- 24.94
- Type
- journal article
- Language
- en
- Open access
- gold
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- Croucher, N. J., Page, A. J., Connor, T. R., Delaney, A. J., Keane, J. A., Bentley, S. D., Parkhill, J., & Harris, S. R. (2015). Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Research. https://doi.org/10.1093/nar/gku1196
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