Who is Who in Phylogenetic Networks

Publication no #2206   Type :   Html | Bib | Both

Created: 2012-04-07 00:46:13     Modified: 2012-09-16 07:14:56

2206 Tetsuo Asano, Jesper Jansson, Kunihiko Sadakane, Ryuhei Uehara and Gabriel Valiente. Faster computation of the Robinson–Foulds distance between phylogenetic networks. In Information Sciences, Vol. 197:77-90, 2012. Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread.         Toggle abstract "The Robinson-Foulds distance, a widely used metric for comparing phylogenetic trees, has recently been generalized to phylogenetic networks. Given two phylogenetic networks N 1, N 2 with n leaf labels and at most m nodes and e edges each, the Robinson-Foulds distance measures the number of clusters of descendant leaves not shared by N 1 and N 2. The fastest known algorithm for computing the Robinson-Foulds distance between N 1 and N 2 runs in O(me) time. In this paper, we improve the time complexity to O(ne/log n) for general phylogenetic networks and O(nm/log n) for general phylogenetic networks with bounded degree (assuming the word RAM model with a word length of ⌈logn⌉ bits), and to optimal O(m) time for leaf-outerplanar networks as well as optimal O(n) time for level-1 phylogenetic networks (that is, galled-trees). 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 network is at most k + 1, which implies that for one level-1 and one level-k phylogenetic network, our algorithm runs in O((k + 1)e) time. © 2012 Elsevier Inc. All rights reserved." @Article{AJSUV2012,       AUTHOR = {Asano, Tetsuo and Jansson, Jesper and Sadakane, Kunihiko and Uehara, Ryuhei and Valiente, Gabriel},       TITLE = {Faster computation of the Robinson{\^a}��Foulds distance between phylogenetic networks},       YEAR = {2012},       JOURNAL = {Information Sciences},       VOLUME = {197},       PAGES = {77-90},       URL = {http://dx.doi.org/10.1016/j.ins.2012.01.038},       KEYWORDS = {distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread} }