Properties of the generalized Robinson-Foulds metric

Borozan, L.; Matijevic, D. and Canzar, S. (2019): Properties of the generalized Robinson-Foulds metric. In: 2019 42Nd International Convention on Information and Communication Technology, Electronics and Microelectronics (Mipro): pp. 330-335

Abstract

Comparing hierarchical structures is a problem with many applications in various fields of biology. In this work we address the problem of comparing phylogenetic trees and quantifying their dissimilarities. The most commonly applied measure of similarity between phylogenetic trees is the Robinson Foulds (RF) metric. The Jaccard-Robinson-Foulds (JRF) metric (of order k) has been recently proposed as a generalization of the RF metric that preserves its widely appreciated properties but increases its resolution and robustness. Here, we conduct thorough experimental analysis of the JRF metric and variations thereof on both real world and simulated data. Our main aim is to deepen the understanding of the properties of this generalized RF metric in comparison to the classical RF metric and other matching based distance measures. To compute the JRF distance between trees, we employ the recently proposed branch-and-cut solver Trajan.

• Item Type: Journal article
• Faculties: Chemistry and Pharmacy > Department of Biochemistry
• Subjects: 500 Science > 540 Chemistry
• Language: English