Efficient Algorithms for Constructing Phylogenetic Networks with Restricted Recombinations

A current high-priority phase of human genomics involves the development of a full Haplotype Map of the human genome [15]. It will be used in largescale screens of populations to associate specific haplotypes with specific complex genetic-influenced diseases. Phylogenetic networks are models of sequence evolution that go beyond trees, allowing biological operations that are not tree-like. The problem is to find a phylogenetic network that derives an input set of sequences. Recently Ding and Gusfield [4] propose a linear time algorithm for theperfect phylogeny tree inference problem. In this paper, we generalize the linear time tree inference algorithm as the base case and propose efficient algorithms that infer phylogenetic networks satisfying given pre-specified types and/or conditions of recombination by using the conflict tabledata struc-