Who is Who in Phylogenetic Networks

Publications of Peter J. Humphries     Order by:   Type | Year

Associated keywords

agreement-forest APX-hard characterization cherry-picking explicit-network from-rooted-trees hybridization minimum-number NP-complete phylogenetic-network phylogeny reconstruction SPR-distance time-consistent-network

Article (Journal)

1 Peter J. Humphries, Simone Linz and Charles Semple. On the complexity of computing the temporal hybridization number for two phylogenies. In DAM, Vol. 161:871-880, 2013. Keywords: agreement forest, APX hard, characterization, from rooted trees, hybridization, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network. Note: http://ab.inf.uni-tuebingen.de/people/linz/publications/TAFapx.pdf.         Toggle abstract "Phylogenetic networks are now frequently used to explain the evolutionary history of a set of species for which a collection of gene trees, reconstructed from genetic material of different parts of the species' genomes, reveal inconsistencies. However, in the context of hybridization, the reconstructed networks are often not temporal. If a hybridization network is temporal, then it satisfies the time constraint of instantaneously occurring hybridization events; i.e. all species that are involved in such an event coexist in time. Furthermore, although a collection of phylogenetic trees can often be merged into a hybridization network that is temporal, many algorithms do not necessarily find such a network since their primary optimization objective is to minimize the number of hybridization events. In this paper, we present a characterization for when two rooted binary phylogenetic trees admit a temporal hybridization network. Furthermore, we show that the underlying optimization problem is APX-hard and, therefore, NP-hard. Thus, unless P=NP, it is unlikely that there are efficient algorithms for either computing an exact solution or approximating it within a ratio arbitrarily close to one. © 2012 Elsevier B.V. All rights reserved." 2 Peter J. Humphries, Simone Linz and Charles Semple. Cherry picking: a characterization of the temporal hybridization number for a set of phylogenies. In BMB, Vol. 75(10):1879-1890, 2013. Keywords: characterization, cherry-picking, from rooted trees, hybridization, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network. Note: http://ab.inf.uni-tuebingen.de/people/linz/publications/CPSpaper.pdf.         Toggle abstract "Recently, we have shown that calculating the minimum-temporal-hybridization number for a set P of rooted binary phylogenetic trees is NP-hard and have characterized this minimum number when P consists of exactly two trees. In this paper, we give the first characterization of the problem for P being arbitrarily large. The characterization is in terms of cherries and the existence of a particular type of sequence. Furthermore, in an online appendix to the paper, we show that this new characterization can be used to show that computing the minimum-temporal hybridization number for two trees is fixed-parameter tractable. © 2013 Society for Mathematical Biology." 3 Peter J. Humphries and Charles Semple. Note on the hybridization number and subtree distance in phylogenetics. In Applied Mathematics Letters, Vol. 22(4):611-615, 2009. Keywords: explicit network, minimum number, phylogenetic network, phylogeny, SPR distance. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/HS08.pdf.