New Algorithms for the Genomic Duplication Problem

Abstract

One of evolutionary molecular biology fundamental issues is to discover genomic duplication events and their correspondence to the species tree. Such events can be reconstructed by clustering single gene duplications that are inferred by reconciling a set of gene trees with a species tree. Here we propose the first solution to the genomic duplication problem in which every reconciliation with the minimal number of single gene duplications is allowed and the method of clustering called minimum episodes under the assumption that input gene trees are unrooted. We also present an evaluation study of proposed algorithms on empirical datasets.