The perfect phylogeny problem is a classic problem in computational biology, where we seek an unrooted phylogeny that is compatible with a set of qualitative characters. Such a tree exists precisely when an intersection graph associated with the character set, called the partition intersection graph, can be triangulated using a restricted set of fill edges. Semple and Steel used the partition intersection graph to characterize when a character set has a unique perfect phylogeny. Bordewich, Huber, and Semple showed how to use the partition intersection graph to find a maximum compatible set of characters. In this paper, we build on these results, characterizing when a unique perfect phylogeny exists for a subset of partial characters. Our characterization is stated in terms of minimal triangulations of the partition intersection graph that are uniquely representable, also known as ur-chordal graphs. Our characterization is motivated by the structure of ur-chordal graphs, and the fact that the block structure of minimal triangulations is mirrored in the graph that has been triangulated.

Kloks, Kratsch, and Spinrad showed how treewidth and minimum-fill, NP-hard combinatorial optimization problems related to minimal triangulations, are broken into subproblems by block subgraphs defined by minimal separators. These ideas were expanded on by Bouchitt e and Todinca, who used potential maximal cliques to solve these problems using a dynamic programming approach in time polynomial in the number of minimal separators of a graph. It is known that solutions to the perfect phylogeny problem, maximum compatibility problem, and unique perfect phylogeny problem are characterized by minimal triangulations of the partition intersection graph. In this paper, we show that techniques similar to those proposed by Bouchitt e and Todinca can be used to solve the perfect phylogeny problem with missing data, the two- state maximum compatibility problem with missing data, and the unique perfect phylogeny problem with missing data in time polynomial in the number of minimal separators of the partition intersection graph.

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 to efficiently 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.