A robinson-foulds measure to compare unrooted trees with rooted trees

Abstract

The Robinson-Foulds (RF) distance is a well-established measure for the comparative analysis of phylogenetic trees, and comparing unrooted gene trees with rooted species trees is a standard application in phylogenetics. However, the RF distance is not defined to compare unrooted trees with rooted trees. Here we propose urRF a new measure based on the standard RF distance to compare an unrooted tree with a rooted tree, and describe a linear time algorithm to compute urRF. Further, we show that our measure relates to several intriguing properties that can be crucial for the in-depth comparative study and the credible rooting of trees. Finally, we present detailed empirical studies based on real data sets demonstrating the performance of our novel RF measure, the efficiency of our linear time algorithm and the quality of determining optimal rootings of unrooted gene trees. © 2012 Springer-Verlag.