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http://hdl.handle.net/10119/9859
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| Title: | Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks |
| Authors: | Asano, Tetsuo
Jansson, Jesper
Sadakane, Kunihiko
Uehara, Ryuhei
Valiente, Gabriel |
| Keywords: | Robinson-Foulds distance
phylogenetic tree
phylogenetic network
polynomial time algorithm |
| Issue Date: | 2010 |
| Publisher: | Springer |
| Magazine name: | Lecture Notes in Computer Science |
| Volume: | 6129/2010 |
| Start page: | 190 |
| End page: | 201 |
| DOI: | 10.1007/978-3-642-13509-5_18 |
| 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. |
| Rights: | This is the author-created version of Springer, Tetsuo Asano, Jesper Jansson, Kunihiko Sadakane, Ryuhei Uehara, and Gabriel Valiente, Lecture Notes in Computer Science, 6129/2010, 2010, 190-201. The original publication is available at www.springerlink.com, http://dx.doi.org/10.1007/978-3-642-13509-5_18 |
| URI: | http://hdl.handle.net/10119/9859 |
| Material Type: | author |
| Appears in Collections: | b10-1. 雑誌掲載論文 (Journal Articles)
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