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Issue No. 02 - April-June (2009 vol. 6)
ISSN: 1545-5963
pp: 221-231
Mukul S. Bansal , Iowa State University, Ames
Oliver Eulenstein , Iowa State University, Ames
André Wehe , Iowa State University, Ames
The gene-duplication problem is to infer a species supertree from a collection of gene trees that are confounded by complex histories of gene-duplication events. This problem is NP-complete and thus requires efficient and effective heuristics. Existing heuristics perform a stepwise search of the tree space, where each step is guided by an exact solution to an instance of a local search problem. A classical local search problem is the {\tt NNI} search problem, which is based on the nearest neighbor interchange operation. In this work, we 1) provide a novel near-linear time algorithm for the {\tt NNI} search problem, 2) introduce extensions that significantly enlarge the search space of the {\tt NNI} search problem, and 3) present algorithms for these extended versions that are asymptotically just as efficient as our algorithm for the {\tt NNI} search problem. The exceptional speedup achieved in the extended {\tt NNI} search problems makes the gene-duplication problem more tractable for large-scale phylogenetic analyses. We verify the performance of our algorithms in a comparison study using sets of large randomly generated gene trees.
Computational phylogenetics, gene-duplication, supertrees, local search, {\tt NNI}.

A. Wehe, O. Eulenstein and M. S. Bansal, "The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. , pp. 221-231, 2009.
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