Who is Who in Phylogenetic Networks

Publications of Chris Whidden     Order by:   Type | Year

Associated keywords

agreement-forest approximation ARG explicit-network FPT from-rooted-trees from-sequences hybridization minimum-number phylogenetic-network phylogeny Program-HybridInterleave reconstruction SPR-distance

Article (Journal)

1 Julia Matsieva, Steven Kelk, Celine Scornavacca, Chris Whidden and Dan Gusfield. A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. In TCBB, Vol. 14(2):404-417, 2017. Keywords: ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny.         2 Leo van Iersel, Steven Kelk, Nela Lekic, Chris Whidden and Norbert Zeh. Hybridization Number on Three Rooted Binary Trees is EPT. In SIDMA, Vol. 30(3):1607-1631, 2016. Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/1402.2136.         3 Chris Whidden, Robert G. Beiko and Norbert Zeh. Fixed-Parameter Algorithms for Maximum Agreement Forests. In SICOMP, Vol. 42(4):1431-1466, 2013. Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance. Note: http://arxiv.org/abs/1108.2664, slides.         Toggle abstract "We present new and improved fixed-parameter algorithms for computing maximum agreement forests of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree prune-and-regraft distance and, if the agreement forest is acyclic, to their hybridization number. These distance measures are essential tools for understanding reticulate evolution. Our algorithm for computing maximum acyclic agreement forests is the first depth-bounded search algorithm for this problem. Our algorithms substantially outperform the best previous algorithms for these problems. © 2013 Society for Industrial and Applied Mathematics."

InProceedings

4 Chris Whidden, Robert G. Beiko and Norbert Zeh. Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments. In Proceedings of the ninth International Symposium on Experimental Algorithms (SEA'10), Vol. 6049:141-153 of LNCS, springer, 2010. Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance. Note: https://www.cs.dal.ca/sites/default/files/technical_reports/CS-2010-03.pdf.         Toggle abstract "We improve on earlier FPT algorithms for computing a rooted maximum agreement forest (MAF) or a maximum acyclic agreement forest (MAAF) of a pair of phylogenetic trees. Their sizes give the subtree-prune-and-regraft (SPR) distance and the hybridization number of the trees, respectively. We introduce new branching rules that reduce the running time of the algorithms from O(3 kn) and O(3 kn log n) to O(2.42 kn) and O(2.42 kn log n), respectively. In practice, the speed up may be much more than predicted by the worst-case analysis.We confirm this intuition experimentally by computing MAFs for simulated trees and trees inferred from protein sequence data. We show that our algorithm is orders of magnitude faster and can handle much larger trees and SPR distances than the best previous methods, treeSAT and sprdist. © Springer-Verlag Berlin Heidelberg 2010." 5 Chris Whidden and Norbert Zeh. A Unifying View on Approximation and FPT of Agreement Forests. In WABI09, Vol. 5724:390-402 of LNCS, Springer, 2009. Keywords: agreement forest, approximation, explicit network, FPT, minimum number, phylogenetic network, phylogeny, reconstruction. Note: https://www.cs.dal.ca/sites/default/files/technical_reports/CS-2009-02.pdf.         Toggle abstract "We provide a unifying view on the structure of maximum (acyclic) agreement forests of rooted and unrooted phylogenies. This enables us to obtain linear- or O(n log n)-time 3-approximation and improved fixed-parameter algorithms for the subtree prune and regraft distance between two rooted phylogenies, the tree bisection and reconnection distance between two unrooted phylogenies, and the hybridization number of two rooted phylogenies. © 2009 Springer Berlin Heidelberg."

MastersThesis

6 Chris Whidden. A Unifying View on Approximation and FPT of Agreement Forests. Master's thesis, Dalhousie University, Canada, 2009. Keywords: agreement forest, approximation, explicit network, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, reconstruction, SPR distance. Note: http://web.cs.dal.ca/~whidden/MCSThesis09.pdf.

PhdThesis

7 Chris Whidden. Efficient Computation and Application of Maximum Agreement Forests. PhD thesis, Dalhousie University, Canada, 2013. Keywords: agreement forest, explicit network, FPT, from rooted trees, minimum number, phylogenetic network, phylogeny, reconstruction. Note: http://hdl.handle.net/10222/35349.