Abstract
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 n 2/logn, 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.
This research was supported in part by NSF grant no. 0334832.
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Bansal, M.S., Eulenstein, O. (2007). An Ω(n
2/logn) Speed-Up of 
Heuristics for the Gene-Duplication Problem.
In: Giancarlo, R., Hannenhalli, S. (eds) Algorithms in Bioinformatics. WABI 2007. Lecture Notes in Computer Science(), vol 4645. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74126-8_12
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DOI: https://doi.org/10.1007/978-3-540-74126-8_12
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