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Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem

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4 Author(s)
Nguyen, C.T. ; Nat. Uni. of Singapore, Singapore ; Nguyen Bao Nguyen ; Wing-Kin Sung ; Louxin Zhang

The small parsimony problem is studied for reconstructing recombination networks from sequence data. The small parsimony problem is polynomial-time solvable for phylogenetic trees. However, the problem is proven NP-hard even for galled recombination networks. A dynamic programming algorithm is also developed to solve the small parsimony problem. It takes O(dn23 h ) time on an input recombination network over length-d sequences in which there are h recombination and n -h tree nodes.

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Computational Biology and Bioinformatics, IEEE/ACM Transactions on  (Volume:4 ,  Issue: 3 )