The DOI matches its Crossref record; 21 of the 21 references it cites were found in a registry or an index.
STEM: species tree estimation using maximum likelihood for gene trees under coalescence
Open accessAbstract
Summary: STEM is a software package written in the C language to obtain maximum likelihood (ML) estimates for phylogenetic species trees given a sample of gene trees under the coalescent model. It includes options to compute the ML species tree, search the space of all species trees for the k trees of highest likelihood and compute ML branch lengths for a user-input species tree. Availability: The STEM package, including source code, is freely available at http://www.stat.osu.edu/~lkubatko/software/STEM/. Contact: lkubatko@stat.osu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
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Swofford, D. L. (2001) · Cited by 12,789
PAUP * [Phylogenetic Analysis Using Parsimony (and Other Methods)]
Cummings, M. P. (2004) · Dictionary of Bioinformatics and Computational Biology · doi:10.1002/0471650129.dob0522 · Cited by 5,215
On the number of segregating sites in genetical models without recombination
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Maddison, W. P. (1997) · Systematic Biology · doi:10.1093/sysbio/46.3.523 · Cited by 3,021
Kingman, J. F. C. (1982) · Stochastic Processes and their Applications · doi:10.1016/0304-4149(82)90011-4 · Cited by 2,155
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Genome-scale approaches to resolving incongruence in molecular phylogenies.
Rokas, A., Williams, B. L., King, N., & Carroll, S. B. (2003) · Nature · doi:10.1038/nature02053 · Cited by 1,512
Rannala, B., & Yang, Z. (2003) · Genetics · doi:10.1093/genetics/164.4.1645 · Cited by 1,131
Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence
Kubatko, L. S., & Degnan, J. H. (2007) · Systematic Biology · doi:10.1080/10635150601146041 · Cited by 1,034
Self-citationChen, F.-C., & Li, W.-H. (2001) · The American Journal of Human Genetics · doi:10.1086/318206 · Cited by 720
Cited by
Bayesian inference of species trees from multilocus data
Heled, J., & Drummond, A. J. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msp274 · Cited by 2,453
How to fail at species delimitation
Carstens, B. C., Pelletier, T. A., Reid, N. M., & Satler, J. D. (2013) · Molecular Ecology · doi:10.1111/mec.12413 · Cited by 1,248
Self-citationBryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N. A., & RoyChoudhury, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss086 · Cited by 965
The BPP program for species tree estimation and species delimitation
Yang, Z. (2015) · Current Zoology · doi:10.1093/czoolo/61.5.854 · Cited by 772
Ecological opportunity and the origin of adaptive radiations
YODER, J. B., CLANCEY, E., DES ROCHES, S., EASTMAN, J. M., GENTRY, L., GODSOE, W., HAGEY, T. J., JOCHIMSEN, D., OSWALD, B. P., ROBERTSON, J., et al. (2010) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2010.02029.x · Cited by 731
Metadata
- Authors
- Kubatko, L. S., Carstens, B. C., & Knowles, L. L.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-02-10
- Volume
- 25
- Issue
- 7
- Pages
- 971-973
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2114227052
- Cited by
- 454
- References
- 21
- FWCI
- 14.88
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Kubatko, L. S., Carstens, B. C., & Knowles, L. L. (2009). STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics. https://doi.org/10.1093/bioinformatics/btp079
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
