Inicio  /  Algorithms  /  Vol: 12 Par: 3 (2019)  /  Artículo
ARTÍCULO
TITULO

Tree Compatibility, Incomplete Directed Perfect Phylogeny, and Dynamic Graph Connectivity: An Experimental Study

David Fernández-Baca and Lei Liu    

Resumen

We study two problems in computational phylogenetics. The first is tree compatibility. The input is a collection ?? 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 ?? 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.

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