Who is Who in Phylogenetic Networks

Publication no #479   Type :   Html | Bib | Both

Created: 2007-11-17 01:16:43     Modified: 2013-06-30 07:43:29

479 Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. In SICOMP, Vol. 35(5):1098-1121, 2006. Keywords: approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://www.df.lth.se/~jj/Publications/triplets_to_gn7_SICOMP2006.pdf.         Toggle abstract "This paper considers the problem of determining whether a given set Τ of rooted triplets can be merged without conflicts into a galled phylogenetic network and, if so, constructing such a network. When the input Τ is dense, we solve the problem in O(|Τ|) time, which is optimal since the size of the input is Θ(|Τ|). In comparison, the previously fastest algorithm for this problem runs in O(|Τ|2) time. We also develop an optimal O(|Τ|)-time algorithm for enumerating all simple phylogenetic networks leaf-labeled by L that are consistent with Τ, where L is the set of leaf labels in Τ, which is used by our main algorithm. Next, we prove that the problem becomes NP-hard if extended to nondense inputs, even for the special case of simple phylogenetic networks. We also show that for every positive integer n, there exists some set Τ of rooted triplets on n leaves such that any galled network can be consistent with at most 0.4883 ·|Τ| of the rooted triplets in Τ. On the other hand, we provide a polynomial-time approximation algorithm that always outputs a galled network consistent with at least a factor of 5/12 (> 0.4166) of the rooted triplets in Τ. © 2006 Society for Industrial and Applied Mathematics." @Article{JNS2006,       AUTHOR = {Jansson, Jesper and Nguyen, Nguyen Bao and Sung, Wing-Kin},       TITLE = {Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network},       YEAR = {2006},       JOURNAL = {SICOMP},       VOLUME = {35},       NUMBER = {5},       PAGES = {1098-1121},       URL = {http://dx.doi.org/10.1137/S0097539704446529},       NOTE = {http://www.df.lth.se/~jj/Publications/triplets_to_gn7_SICOMP2006.pdf},       KEYWORDS = {approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction} }