Tree compatibility, incomplete directed perfect phylogeny, and dynamic graph connectivity: an experimental study (Q2312406)

Summary: We study two problems in computational phylogenetics. The first is tree compatibility. The input is a collection \(\mathcal{P}\) of phylogenetic trees over different partially-overlapping sets of species. The goal is to find a single phylogenetic tree that displays all the evolutionary relationships implied by \(\mathcal{P}\). The second problem is incomplete directed perfect phylogeny (IDPP). The input is a data matrix describing a collection of species by a set of characters, where some of the information is missing. The question is whether there exists a way to fill in the missing information so that the resulting matrix can be explained by a phylogenetic tree satisfying certain conditions. We explain the connection between tree compatibility and IDPP and show that a recent tree compatibility algorithm is effectively a generalization of an earlier IDPP algorithm. Both algorithms rely heavily on maintaining the connected components of a graph under a sequence of edge and vertex deletions, for which they use the dynamic connectivity data structure of Holm et al., known as HDT. We present a computational study of algorithms for tree compatibility and IDPP. We show experimentally that substituting HDT by a much simpler data structure -- essentially, a single-level version of HDT -- improves the performance of both of these algorithm in practice. We give partial empirical and theoretical justifications for this observation.