Who is Who in Phylogenetic Networks

Publications related to 'simulation' : Articles which deal with creating realistic phylogenetic networks.   Order by:   Type | Year

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Associated keywords

abstract-network coalescent evaluation explicit-network from-network from-sequences galled-tree generation hybridization incomplete-lineage-sorting lateral-gene-transfer phylogenetic-network phylogeny Program-Hybrid-Lambda Program-NetGen Program-PhyloNet Program-PhyloNetworks-SNaQ Program-Recodon reconstruction regular-network simulation software statistical-model tree-sibling-network tree-child-network unicyclic-network

Article (Journal)

1 Miguel Arenas, Gabriel Valiente and David Posada. Characterization of reticulate networks based on the coalescent with recombination. In MBE, Vol. 25(12):2517-2520, 2008. Keywords: coalescent, evaluation, explicit network, galled tree, phylogenetic network, phylogeny, Program Recodon, regular network, simulation, tree sibling network, tree-child network. Note: http://dx.doi.org/10.1093/molbev/msn219.         Toggle abstract "Phylogenetic networks aim to represent the evolutionary history of taxa. Within these, reticulate networks are explicitly able to accommodate evolutionary events like recombination, hybridization, or lateral gene transfer. Although several metrics exist to compare phylogenetic networks, they make several assumptions regarding the nature of the networks that are not likely to be fulfilled by the evolutionary process. In order to characterize the potential disagreement between the algorithms and the biology, we have used the coalescent with recombination to build the type of networks produced by reticulate evolution and classified them as regular, tree sibling, tree child, or galled trees. We show that, as expected, the complexity of these reticulate networks is a function of the population recombination rate. At small recombination rates, most of the networks produced are already more complex than regular or tree sibling networks, whereas with moderate and large recombination rates, no network fit into any of the standard classes. We conclude that new metrics still need to be devised in order to properly compare two phylogenetic networks that have arisen from reticulating evolutionary process. © 2008 The Authors." 2 Miguel Arenas. Computer programs and methodologies for the simulation of DNA sequence data with recombination. In Frontiers in Genetics, Vol. 4(9), 2013. Keywords: explicit network, phylogenetic network, phylogeny, simulation. Note: http://dx.doi.org/10.3389%2Ffgene.2013.00009.         3 Sha Zhu, James H. Degnan, Sharyn J. Goldstein and Bjarki Eldon. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. In BMCB, Vol. 16(292):1-7, 2015. Keywords: explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software. Note: http://dx.doi.org/10.1186/s12859-015-0721-y.         4 Hussein A. Hejase and Kevin J. Liu. A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. Vol. 17(422):1-12, 2016. Keywords: abstract network, evaluation, from sequences, phylogenetic network, phylogeny, Program PhyloNet, Program PhyloNetworks SNaQ, reconstruction, simulation, unicyclic network. Note: http://dx.doi.org/10.1186/s12859-016-1277-1.         5 Olga K. Kamneva and Noah A. Rosenberg. Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting. In Evolutionary Bioinformatics, Vol. 13(1176934317691935):1-16, 2017. Keywords: evaluation, explicit network, incomplete lineage sorting, simulation. Note: https://dx.doi.org/10.1177%2F1176934317691935.

PhdThesis

6 Monique M. Morin. Phylogenetic Networks: Simulation, Characterization, and Reconstruction. PhD thesis, The University of New Mexico, U.S.A., 2007. Keywords: evaluation, explicit network, hybridization, lateral gene transfer, phylogenetic network, phylogeny, Program NetGen, simulation, software. Note: http://www.cs.unm.edu/~morin/morin_phd.pdf.         7 Sha Zhu. Stochastic tree models and probabilistic modelling of gene trees of given species networks. PhD thesis, University of Canterbury, New Zealand, 2013. Keywords: from network, generation, phylogenetic network, phylogeny, simulation, statistical model. Note: http://hdl.handle.net/10092/7944.

Misc

8 Sha Zhu, James H. Degnan and Bjarki Eldon. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. 2013. Keywords: explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software. Note: http://arxiv.org/abs/1303.0673.