The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent
Open accessAbstract
The multispecies coalescent provides a natural framework for accommodating ancestral genetic polymorphism and coalescent processes that can cause different genomic regions to have different genealogical histories. The Bayesian program BPP includes a full-likelihood implementation of the multispecies coalescent, using transmodel Markov chain Monte Carlo to calculate the posterior probabilities of different species trees. BPP is suitable for analyzing multilocus sequence data sets and it accommodates the heterogeneity of gene trees (both the topology and branch lengths) among loci and gene tree uncertainties due to limited phylogenetic information at each locus. Here, we provide a practical guide to the use of BPP in species tree estimation. BPP is a command-line program that runs on linux, macosx, and windows. This protocol shows how to use both BPP 3.4 (http://abacus.gene.ucl.ac.uk/software/) and BPP 4.0 (https://github.com/bpp/).
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Cites
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
(1964) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3210-2.50006-6 · Cited by 3,059
Maddison, W. P. (1997) · Systematic Biology · doi:10.1093/sysbio/46.3.523 · Cited by 3,021
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960
Self-citationGenetic history of an archaic hominin group from Denisova Cave in Siberia
Reich, D., Green, R. E., Kircher, M., Krause, J., Patterson, N., Durand, E. Y., Viola, B., Briggs, A. W., Stenzel, U., Johnson, P. L. F., et al. (2010) · Nature · doi:10.1038/nature09710 · Cited by 1,991
Gene tree discordance, phylogenetic inference and the multispecies coalescent
Degnan, J. H., & Rosenberg, N. A. (2009) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2009.01.009 · Cited by 1,958
Bayesian species delimitation using multilocus sequence data
Yang, Z., & Rannala, B. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0913022107 · Cited by 1,405
Self-citationRannala, B., & Yang, Z. (2003) · Genetics · doi:10.1093/genetics/164.4.1645 · Cited by 1,131
Self-citationEstimating the pattern of nucleotide substitution
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00178256 · Cited by 1,076
Self-citationIs a new and general theory of molecular systematics emerging?
Edwards, S. V. (2009) · Evolution · doi:10.1111/j.1558-5646.2008.00549.x · Cited by 1,040
Cited by
Phylogenetic tree building in the genomic age
Kapli, P., Yang, Z., & Telford, M. J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0233-0 · Cited by 533
Self-citationYan, H., Hu, Z., Thomas, G. W. C., Edwards, S. V., Sackton, T. B., & Liu, J. S. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad195 · Cited by 28
Metadata
- Authors
- Flouri, T., Jiao, X., Rannala, B., & Yang, Z.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-07-23
- Volume
- 35
- Issue
- 10
- Pages
- 2585-2593
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2883170162
- Cited by
- 445
- References
- 39
- FWCI
- 10.44
- Type
- journal article
- Language
- en
- Open access
- hybrid
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