Who is Who in Phylogenetic Networks

Publication no #1996   Type :   Html | Bib | Both

Created: 2010-03-23 17:51:59     Modified: 2012-09-16 07:16:36

1996 Tetsuo Asano, Jesper Jansson, Kunihiko Sadakane, Ryuhei Uehara and Gabriel Valiente. Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks. In CPM10, Vol. 6129:190-201 of LNCS, springer, 2010. Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread. Note: http://hdl.handle.net/10119/9859, slides available at http://cs.nyu.edu/parida/CPM2010/MainPage_files/18.pdf.         Toggle 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 N1,N2 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 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. © Springer-Verlag Berlin Heidelberg 2010." @InProceedings{AJSUV2010,       AUTHOR = {Asano, Tetsuo and Jansson, Jesper and Sadakane, Kunihiko and Uehara, Ryuhei and Valiente, Gabriel},       TITLE = {Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks},       YEAR = {2010},       BOOKTITLE = {CPM10},       VOLUME = {6129},       PAGES = {190-201},       SERIES = {LNCS},       PUBLISHER = {springer},       URL = {http://dx.doi.org/10.1007/978-3-642-13509-5_18},       NOTE = {http://hdl.handle.net/10119/9859, slides available at http://cs.nyu.edu/parida/CPM2010/MainPage_files/18.pdf},       KEYWORDS = {distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread} }