Who is Who in Phylogenetic Networks

Publications of Josh Voorkamp né Collins     Order by:   Type | Year

Associated keywords

agreement-forest explicit-network FPT from-rooted-trees from-unrooted-trees generation hybridization minimum-number phylogenetic-network phylogeny Program-HybridInterleave reconstruction software

2014

1 Josh Voorkamp né Collins. Untangling Evolution. PhD thesis, University of Otago, New Zealand, 2014. Keywords: agreement forest, explicit network, from rooted trees, generation, phylogenetic network, phylogeny, reconstruction. Note: http://otago.ourarchive.ac.nz/handle/10523/4802.         2 Josh Voorkamp né Collins. Maximal Acyclic Agreement Forests. In JCB, Vol. 21(10):723-731, 2014. Keywords: agreement forest, explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction.

2011

3 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."

2009

4 Josh Voorkamp né Collins. Rekernelisation Algorithms in Hybrid Phylogenies. Master's thesis, University of Canterbury, New Zealand, 2009. Keywords: agreement forest, explicit network, FPT, from rooted trees, from unrooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software. Note: http://hdl.handle.net/10092/2852.