Assessing clustering results with reference taxonomies.

The comparative analysis of phylogenies obtained using different phylogenetic methods or different gene sequences for a given set of species, is usually done by computing some quantitative measure of similarity between the phylogenetic trees. Such a quantitative approach provides little insight into the actual similarities and differences between the alternative phylogenies. In this paper, we present a method for the qualitative assessment of a phylogenetic tree against a reference taxonomy, based on highlighting their common clusters. Our algorithms build a reference taxonomy for the taxa present in a given phylogenetic tree and produce a dendogram for the input phylogenetic tree, with branches in those clusters common to the reference taxonomy highlighted. Our implementation of the algorithms produces publication-quality graphics. For unrooted phylogenies, the method produces a radial cladogram for the input phylogenetic tree, with branches in common clusters to the reference taxonomy highlighted.