![]() We present a computational study of algorithms for tree compatibility and IDPP. 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 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. 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. The input is a data matrix describing a collection of species by a set of characters, where some of the information is missing. The second problem is incomplete directed perfect phylogeny (IDPP). The goal is to find a single phylogenetic tree that displays all the evolutionary relationships implied by P. The input is a collection P of phylogenetic trees over different partially-overlapping sets of species. ![]() We study two problems in computational phylogenetics. ![]()
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