The DOI matches its Crossref record; 50 of the 50 references it cites were found in a registry or an index.
Fast hierarchical Bayesian analysis of population structure
Open accessAbstract
We present fastbaps, a fast solution to the genetic clustering problem. Fastbaps rapidly identifies an approximate fit to a Dirichlet process mixture model (DPM) for clustering multilocus genotype data. Our efficient model-based clustering approach is able to cluster datasets 10-100 times larger than the existing model-based methods, which we demonstrate by analyzing an alignment of over 110 000 sequences of HIV-1 pol genes. We also provide a method for rapidly partitioning an existing hierarchy in order to maximize the DPM model marginal likelihood, allowing us to split phylogenetic trees into clades and subclades using a population genomic model. Extensive tests on simulated data as well as a diverse set of real bacterial and viral datasets show that fastbaps provides comparable or improved solutions to previous model-based methods, while being significantly faster. The method is made freely available under an open source MIT licence as an easy to use R package at https://github.com/gtonkinhill/fastbaps.
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Cites
A new look at the statistical model identification
Akaike, H. (1974) · IEEE Transactions on Automatic Control · doi:10.1109/tac.1974.1100705 · Cited by 51,879
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Pritchard, J. K., Stephens, M., & Donnelly, P. (2000) · Genetics · doi:10.1093/genetics/155.2.945 · Cited by 33,908
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genalex 6: genetic analysis in Excel. Population genetic software for teaching and research
PEAKALL, R., & SMOUSE, P. E. (2006) · Molecular Ecology Notes · doi:10.1111/j.1471-8286.2005.01155.x · Cited by 16,589
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
Fast model-based estimation of ancestry in unrelated individuals
Alexander, D. H., Novembre, J., & Lange, K. (2009) · Genome Research · doi:10.1101/gr.094052.109 · Cited by 9,898
UMAP: Uniform Manifold Approximation and Projection
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UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction
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Dimensionality reduction for visualizing single-cell data using UMAP
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Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design
Shao, Y., Wang, S., Gichuki, B. M., Stares, M. D., Rozday, T. J., Kumar, N., Browne, H. P., Dawson, N. J. R., Njunge, J. M., Tigoi, C., et al. (2026) · Cell · doi:10.1016/j.cell.2026.01.007 · Cited by 17
Genomic Characteristion of Opportunistic Pathogen Kluyvera Reveals a Novel CTX-M Subgroup
Yu, K., Huang, Z., Lan, R., Morris, J. G., Xiao, Y., Fu, S., Gao, H., Bai, X., Li, K., & Wang, D. (2023) · Microorganisms · doi:10.3390/microorganisms11122836 · Cited by 12
Metadata
- Authors
- Tonkin-Hill, G., Lees, J. A., Bentley, S. D., Frost, S. D. W., & Corander, J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-05-11
- Volume
- 47
- Issue
- 11
- Pages
- 5539-5549
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2950753995
- Cited by
- 346
- References
- 50
- FWCI
- 13.00
- Type
- journal article
- Language
- en
- Open access
- gold
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- Tonkin-Hill, G., Lees, J. A., Bentley, S. D., Frost, S. D. W., & Corander, J. (2019). Fast hierarchical Bayesian analysis of population structure. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz361
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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