Degnan Publications of James H. Degnan     Order by:   Type | Year
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Article (Journal)
1
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James H. Degnan. Modeling Hybridization Under the Network Multispecies Coalescent. In SB, Vol. 67(5):786-799, 2018.
Keywords: distance between networks, phylogenetic network, phylogeny, reconstruction, survey.
Note: https://academic.oup.com/sysbio/article/67/5/786/5017269.
       

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Sha Zhu and James H. Degnan. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent. In SB, Vol. 66(2):283-298, 2017.
Keywords: branch length, coalescent, explicit network, from network, likelihood, phylogenetic network, phylogeny, Program Hybrid-coal, Program Hybrid-Lambda, Program PhyloNet, software, uniqueness.
Note: presentation available at https://www.youtube.com/watch?v=JLYGTfEZG7g.
       

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Sha Zhu, James H. Degnan, Sharyn J. Goldstein and Bjarki Eldon. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. In BMCB, Vol. 16(292):1-7, 2015.
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software.
Note: http://dx.doi.org/10.1186/s12859-015-0721-y.
       

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Yun Yu, James H. Degnan and Luay Nakhleh. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. In PLoS Genetics, Vol. 8(4):e1002660, 2012.
Keywords: AIC, BIC, explicit network, hybridization, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1371/journal.pgen.1002660.
       
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Yun Yu, Cuong Than, James H. Degnan and Luay Nakhleh. Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting. In Systematic Biology, Vol. 60(2):138-149, 2011.
Keywords: coalescent, hybridization, lineage sorting, reconstruction, statistical model.
Note: http://www.cs.rice.edu/~nakhleh/Papers/YuEtAl-SB11.pdf.
       
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Misc
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Sha Zhu, James H. Degnan and Bjarki Eldon. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. 2013.
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software.
Note: http://arxiv.org/abs/1303.0673.
       

7
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Sha Zhu, James H. Degnan and Mike Steel. Probabilistic modeling of gene trees given species networks. 2011.
Keywords: from network, generation, phylogenetic network, phylogeny, statistical model.
Note: Poster, http://www.newton.ac.uk/programmes/PLG/Zhu.pdf.