An efficient algorithm for testing the compatibility of phylogenies with nested taxa

Abstract

Background: Semi-labeled trees generalize ordinary phylogenetic trees, allowing internal nodes to be labeled by higher-order taxa. Taxonomies are examples of semi-labeled trees. Suppose we are given collection P of semi-labeled trees over various subsets of a set of taxa. The ancestral compatibility problem asks whether there is a semi-labeled tree that respects the clusterings and the ancestor/descendant relationships implied by the trees in P. The running time and space usage of the best previous algorithm for testing ancestral compatibility depend on the degrees of the nodes in the trees in P. Results: We give a algorithm for the ancestral compatibility problem that runs in O(MP log2 MP) time and uses O(MP) space, where MP is the total number of nodes and edges in the trees in P. Conclusions: Taxonomies enable researchers to expand greatly the taxonomic coverage of their phylogenetic analyses. The running time of our method does not depend on the degrees of the nodes in the trees in P. This characteristic is important when taxonomies-which can have nodes of high degree-are used.