Background: The evolutionary history of organisms can be described by phylogenetic trees. We need to compare the topologies of rooted phylogenetic trees when researching the evolution of a given set of species.
Objective: Up to now, there are several metrics measuring the dissimilarity between rooted phylogenetic trees, and those metrics are defined by different ways.
Methods: This paper analyzes those metrics from their definitions and the distance values computed by those metrics by terms of experiments.
Results: The results of experiments show that the distances calculated by the cluster metric, the partition metric, and the equivalent metric have a good Gaussian fitting, and the equivalent metric can describe the difference between trees better than the others.
Conclusion: Moreover, it presents a tool called as CDRPT (Computing Distance for Rooted Phylogenetic Trees). CDRPT is a web server to calculate the distance for trees by an on-line way. CDRPT can also be off-line used by means of installing application packages for the Windows system. It greatly facilitates the use of researchers. The home page of CDRPT is http://bioinformatics.imu.edu.cn/tree/.