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An Ω(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem
October-December 2008 (vol. 5 no. 4)
pp. 514-524
Mukul S. Bansal, Iowa State University, Ames
Oliver Eulenstein, Iowa State University, Ames
The gene-duplication problem is to infer a species supertree from gene trees that are confounded by complex histories of gene duplications. This problem is NP-hard 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. We improve on the time complexity of the local search problem by a factor of n2= log n, where n is the size of the resulting species supertree. Typically, several thousand instances of the local search problem are solved throughout a stepwise heuristic search. Hence, our improvement makes the gene-duplication problem much more tractable for large-scale phylogenetic analyses.

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Index Terms:
Algorithms, Phylogenetics, Computational Biology, Gene Duplication, Supertrees
Mukul S. Bansal, Oliver Eulenstein, "An Ω(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, no. 4, pp. 514-524, Oct.-Dec. 2008, doi:10.1109/TCBB.2008.69
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