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The gene-duplication problem is to infer a species tree from a collection of gene trees. The decision variant of this problem is NP-complete. The utility of this NP-hard problem for large-scale phylogenetic analyses has been largely limited by the high time complexity of existing heuristics. These methods search the whole possible suptrees. They solve a local search problem instance in each step. The NNI(nearest neighbor interchange) local search problem is a classical local search problem . In this paper, we study the duplication-loss problem and provide a novel algorithm for the k-NNI local search problem. Our improvement not only significantly enlarges the search space but also makes the time complexity better. Hence, the duplication-loss problem will be much more manageable for large scale phylogenetic analyses. KeywordsDuplication-Loss; NNI; Local search; Computational phylogenetics; Computational complexity; Algorithm

A Novel Algorithm for Duplication-Loss Problem Based on NNI Local Search