A Survey of Metrics Measuring Difference for Rooted Phylogenetic Trees

Title:A Survey of Metrics Measuring Difference for Rooted Phylogenetic Trees

Volume: 15 Issue: 7

Author(s): Juan Wang, Xinyue Qi, Bo Cui and Maozu Guo*

Affiliation:

• School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing,China

Keywords: Phylogenetic tree, metric, CDRPT, distance, evolution, topologies.

Abstract:

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/.

Cite this article as:

Wang Juan , Qi Xinyue , Cui Bo and Guo Maozu *, A Survey of Metrics Measuring Difference for Rooted Phylogenetic Trees, Current Bioinformatics 2020; 15 (7) . https://dx.doi.org/10.2174/1574893614666191017130217