Who is Who in Phylogenetic Networks

Publication no #2216   Type :   Html | Bib | Both

Created: 2012-05-16 17:22:28     Modified: 2014-08-19 20:19:06

2216 Leo van Iersel, Steven Kelk, Nela Lekic and Celine Scornavacca. A practical approximation algorithm for solving massive instances of hybridization number. In WABI12, Vol. 7534(430-440) of LNCS, springer, 2012. Keywords: agreement forest, approximation, explicit network, from rooted trees, hybridization, phylogenetic network, phylogeny, Program CycleKiller, Program Dendroscope, Program HybridNET, reconstruction, software. Note: http://arxiv.org/abs/1205.3417.         Toggle abstract "Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two phylogenetic trees is a hard computational problem. In practice, exact solvers struggle to solve instances with reticulation number larger than 40. For such instances, one has to resort to heuristics and approximation algorithms. Here we present the algorithm CycleKiller which is the first approximation algorithm that can produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Theoretically, the algorithm is an exponential-time 2-approximation (or 4-approximation in its fastest mode). However, using simulations we demonstrate that in practice the algorithm runs quickly for large and difficult instances, producing solutions within one percent of optimality. An implementation of this algorithm, which extends the theoretical work of [14], has been made publicly available. © 2012 Springer-Verlag." @InProceedings{IKLS2012,       AUTHOR = {van Iersel, Leo and Kelk, Steven and Lekic, Nela and Scornavacca, Celine},       TITLE = {A practical approximation algorithm for solving massive instances of hybridization number},       YEAR = {2012},       BOOKTITLE = {WABI12},       VOLUME = {7534},       NUMBER = {430-440},       SERIES = {LNCS},       PUBLISHER = {springer},       URL = {http://dx.doi.org/10.1007/978-3-642-33122-0_34},       NOTE = {http://arxiv.org/abs/1205.3417},       KEYWORDS = {agreement forest, approximation, explicit network, from rooted trees, hybridization, phylogenetic network, phylogeny, Program CycleKiller, Program Dendroscope, Program HybridNET, reconstruction, software} }