Juan Wang, Xinyue Qi, Bo Cui and Maozu Guo* Pages 697 - 702 ( 6 )
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/.
Phylogenetic tree, metric, CDRPT, distance, evolution, topologies.
School of Computer Science, Inner Mongolia University, Hohhot, School of Computer Science, Inner Mongolia University, Hohhot, School of Computer Science, Inner Mongolia University, Hohhot, School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing