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 N1,N2with n leaves, m nodes, and e edges, the Robinson-Foulds distance measures the number of clusters of descendant leaves that are not shared by N1 and N2. 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 the minimum 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.
|Name||Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|
|Conference||21st Annual Symposium on Combinatorial Pattern Matching, CPM 2010|
|City||New York, NY|
|Period||21/06/10 → 23/06/10|
- Theoretical Computer Science
- Computer Science(all)