Who is Who in Phylogenetic Networks

Publication no #717   Type :   Html | Bib | Both

Created: 2009-11-17 11:41:02     Modified: 2011-10-17 02:23:26

717 Josh Voorkamp né Collins, Simone Linz and Charles Semple. Quantifying hybridization in realistic time. In JCB, Vol. 18(10):1305-1318, 2011. Keywords: explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software. Note: http://wwwcsif.cs.ucdavis.edu/~linzs/CLS10_interleave.pdf, software available at http://www.math.canterbury.ac.nz/~c.semple/software.shtml.         Toggle abstract "Recently, numerous practical and theoretical studies in evolutionary biology aim at calculating the extent to which reticulation-for example, horizontal gene transfer, hybridization, or recombination-has influenced the evolution for a set of present-day species. It has been shown that inferring the minimum number of hybridization events that is needed to simultaneously explain the evolutionary history for a set of trees is an NP-hard and also fixed-parameter tractable problem. In this article, we give a new fixed-parameter algorithm for computing the minimum number of hybridization events for when two rooted binary phylogenetic trees are given. This newly developed algorithm is based on interleaving-a technique using repeated kernelization steps that are applied throughout the exhaustive search part of a fixed-parameter algorithm. To show that our algorithm runs efficiently to be applicable to a wide range of practical problem instances, we apply it to a grass data set and highlight the significant improvements in terms of running times in comparison to an algorithm that has previously been implemented. © 2011, Mary Ann Liebert, Inc." @Article{CLS2011,       AUTHOR = {Voorkamp n{\~A}� Collins, Josh and Linz, Simone and Semple, Charles},       TITLE = {Quantifying hybridization in realistic time},       YEAR = {2011},       JOURNAL = {JCB},       VOLUME = {18},       NUMBER = {10},       PAGES = {1305-1318},       URL = {http://dx.doi.org/10.1089/cmb.2009.0166},       NOTE = {http://wwwcsif.cs.ucdavis.edu/~linzs/CLS10_interleave.pdf, software available at http://www.math.canterbury.ac.nz/~c.semple/software.shtml},       KEYWORDS = {explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software} }