Practical performance of tree comparison metrics

The phylogenetic literature contains numerous measures for assessing differences between two phylogenetic trees. Individual measures have been criticized on various grounds, but little is known about their comparative performance in typical applications. We evaluate the performance of nine tree distance measures on two tasks: (1) distinguishing trees separated by lesser versus greater numbers of recombinations, and (2) distinguishing trees inferred with lower versus higher quality data. We find that when the trees being compared are similar, measures which make use of branch lengths are superior, with the branch-length version of the Robinson-Foulds metric (Robinson & Foulds, 1979) performing best. In contrast, for dissimilar trees topology-only measures are superior, with the Alignment metric of Nye et al. (2006) performing best. We also apply the measures to a mammalian data set and observe that the best metric depends on whether branch-length information is of interest. We give p...