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Z. Du, Stamatakis, A., Lin, F., Roshan, U., and Nakhleh, L., Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood, in Proceedings of the 2005 International Conference on High Performance Computing and Communications, 2005, vol. 2, pp. 346-350.
L. Nakhleh, Warnow, T., Linder, C. R., and John, S. K., Reconstructing reticulate evolution in species–theory and practice, in Journal of Computational Biology, 2005, vol. 12(6-7), pp. 796-811.
E. Erdem, Lifschitz, V., Nakhleh, L., and Ringe, D., Reconstructing the Evolutionary History of Indo-European Languages using Answer Set Programming, in Proceedings of the Fifth International Symposium on Practical Aspects of Declarative Languages (PADL 2003), 2003, vol. 2562, pp. 160-176.
L. Nakhleh, Sun, J., Warnow, T., Linder, R., Moret, B. M. E., and Tholse, A., Towards the development of tools for evaluating phylogenetic network reconstruction methods, in Proc.\ 8th Pacific Symp. on Biocomputing ({PSB03}), 2003, pp. 315–326.