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D. Wen, Yu, Y., and Nakhleh, L., Bayesian inference of species phylogenies under the multispecies network coalescent, PLoS Genetics, vol. 12, no. 5, p. e1006006, 2016.PDF icon WenEtAl-PLoSGenetics2016.pdf (2.11 MB)
D. Wen, Yu, Y., Hahn, M. W., and Nakhleh, L., Reticulate Evolutionary History and Extensive Introgression in Mosquito Species Revealed by Phylogenetic Network Analysis, Molecular Ecology, vol. 25, pp. 2361-2372, 2016.PDF icon WenEtAl-MolEcol2016.pdf (1.26 MB)
D. Wen, Yu, Y., Zhu, J., and Nakhleh, L., Inferring phylogenetic networks using PhyloNet, Systematic Biology, vol. 67, no. 4, pp. 735-740, 2018.PDF icon phylonet3.pdf (144.21 KB)
D. Wen and Nakhleh, L., Co-estimating reticulate phylogenies and gene trees from multi-locus sequence data, Systematic Biology, vol. 67, no. 3, pp. 439-457, 2018.PDF icon WenNakhleh-SysBio2018PlusSI.pdf (5.92 MB)
T. Warnow, Evans, S. N., Ringe, D., and Nakhleh, L., A Stochastic model of language evolution that incorporates homoplasy and borrowing, Phylogenetic Methods and the Prehistory of Languages, 2004.
Y. Wang, Ogilvie, H. A., and Nakhleh, L., Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees, Molecular Biology and Evolution, vol. 37, pp. 1809-1818, 2020.PDF icon MBE2020.pdf (502.98 KB)
Y. Wang and Nakhleh, L., Towards an Accurate and Efficient Heuristic for Species/Gene Tree Co-estimation, Bioinformatics, vol. 34, pp. i697-i705, 2018.PDF icon WangNakhleh-ECCB18.pdf (1.8 MB)