Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks

• Asano, Tetsuo

• Jansson, Jesper

• Sadakane, Kunihiko

• Uehara, Ryuhei

• Valiente, Gabriel

Abstract

The Robinson-Foulds distance, which is the most widely used metric for comparing phylogenetic trees, has recently been generalized to phylogenetic networks. Given two networks N_1,N_2 with n leaves, m nodes, and e edges, the Robinson-Foulds distance measures the number of clusters of descendant leaves that are not shared by N_1and N_2. The fastest known algorithm for computing the Robinson-Foulds distance between those networks runs in O(m(m+e)) time. In this paper, we improve the time complexity to O(n(m + e)/ log n) for general networks and O(nm/log n) for general networks with bounded degree, and to optimal O(m+e) time for planar phylogenetic networks and boundedlevel phylogenetic networks. We also introduce the natural concept of theminimum spread of a phylogenetic network and show how the running time of our new algorithm depends on this parameter. As an example, we prove that the minimum spread of a level-k phylogenetic network is at most k + 1, which implies that for two level-k phylogenetic networks, our algorithm runs in O((k + 1)(m + e)) time.

Combinatorial Pattern Matching : 21st Annual Symposium, CPM 2010, New York, NY, USA, June 21-23, 2010.

identifier:https://dspace.jaist.ac.jp/dspace/handle/10119/9859

Journal

• Lecture Notes in Computer Science

  Lecture Notes in Computer Science 6129/2010 190-201, 2010

  Springer

Keywords

• Robinson-Foulds distance
• phylogenetic tree
• phylogenetic network
• polynomial time algorithm

Details

• CRID: 1050001337538298496
• NII Article ID: 120003184350
• ISSN: 03029743
• Web Site: http://hdl.handle.net/10119/9859
• Text Lang: en
• Article Type: journal article
• Data Source:
  • IRDB
  • CiNii Articles