Constructing perfect phylogenies and proper triangulations for three-state characters

Abstract

In this paper, we study the problem of constructing perfect phylogenies for three-state characters. Our work builds on two recent results. The first result states that for three-state characters, the local condition of examining all subsets of three characters is sufficient to determine the global property of admitting a perfect phylogeny. The second result applies tools from minimal triangulation theory to the partition intersection graph to determine if a perfect phylogeny exists. Despite the wealth of combinatorial tools and algorithms stemming from the chordal graph and minimal triangulation literature, it is unclear how to use such approaches efficiently to construct a perfect phylogeny for three-state characters when the data admits one. We utilize structural properties of both the partition intersection graph and the original data in order to achieve a competitive time bound. © 2011 Springer-Verlag.