Who is Who in Phylogenetic Networks

Publication no #515   Type :   Html | Bib | Both

Created: 2007-11-17 01:16:44     Modified: 2008-04-02 08:32:41

515 Cam Thach Nguyen, Nguyen Bao Nguyen and Wing-Kin Sung. Fast Algorithms for computing the Tripartition-based Distance between Phylogenetic Networks. In JCO, Vol. 13(3), 2007. Keywords: distance between networks, phylogenetic network, phylogeny, tripartition distance. Note: http://dx.doi.org/10.1007/s10878-006-9025-5.         Toggle abstract "Consider two phylogenetic networks N and N′ of size n. The tripartition-based distance finds the proportion of tripartitions which are not shared by N and N′. This distance is proposed by Moret et al. (2004) and is a generalization of Robinson-Foulds distance, which is orginally used to compare two phylogenetic trees. This paper gives an O(min {kn log n, n log n + hn} -time algorithm to compute this distance, where h is the number of hybrid nodes in N and N′ while k is the maximum number of hybrid nodes among all biconnected components in N and N′. Note that k ≪ h ≪ n in a phylogenetic network. In addition, we propose algorithms for comparing galled-trees, which are an important, biological meaningful special case of phylogenetic network. We give an O(n)-time algorithm for comparing two galled-trees. We also give an O(n + kh)-time algorithm for comparing a galled-tree with another general network, where h and k are the number of hybrid nodes in the latter network and its biggest biconnected component respectively. © Springer Science+Business Media, LLC 2007."