Abstract
MOTIVATION: Deciphering the location of gene duplications and multiple gene duplication episodes on the Tree of Life is fundamental to understanding the way gene families and genomes evolve. The multiple gene duplication problem provides a framework for placing gene duplication events onto nodes of a given species tree, and detecting episodes of multiple gene duplication. One version of the multiple gene duplication problem was defined by Guigó et al. in 1996. Several heuristic solutions have since been proposed for this problem, but no exact algorithms were known. RESULTS: In this article we solve this longstanding open problem by providing the first exact and efficient solution. We also demonstrate the improvement offered by our algorithm over the best heuristic approaches, by applying it to several simulated as well as empirical datasets.