Who is Who in Phylogenetic Networks

Publications related to 'Program Recodon' : Recodon is a population genetic simulator that generates samples of nucleotide and codon sequences from populations with recombination, migration and growth, after generating their genealogy (a phylogenetic network) under the coalescent framework. Available at http://darwin.uvigo.es/software/recodon.html.   Order by:   Type | Year

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Associated keywords

coalescent evaluation explicit-network galled-tree generation level-k-phylogenetic-network phylogenetic-network phylogeny Program-Recodon regular-network simulation software tree-sibling-network tree-child-network

2009

1 Philippe Gambette, Vincent Berry and Christophe Paul. The structure of level-k phylogenetic networks. In CPM09, Vol. 5577:289-300 of LNCS, springer, 2009. Keywords: coalescent, explicit network, galled tree, level k phylogenetic network, phylogenetic network, Program Recodon. Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00371485/en/.         Toggle abstract "Evolution is usually described as a phylogenetic tree, but due to some exchange of genetic material, it can be represented as a phylogenetic network which has an underlying tree structure. The notion of level was recently introduced as a parameter on realistic kinds of phylogenetic networks to express their complexity and tree-likeness. We study the structure of level-k networks, and how they can be decomposed into level-k generators. We also provide a polynomial time algorithm which takes as input the set of level-k generators and builds the set of level-(k + 1) generators. Finally, with a simulation study, we evaluate the proportion of level-k phylogenetic networks among networks generated according to the coalescent model with recombination. © 2009 Springer Berlin Heidelberg."

2008

2 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." 3 Miguel Arenas and David Posada. Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography. In BMCB, Vol. 8(458), 2008. Keywords: coalescent, generation, Program Recodon, software. Note: http://dx.doi.org/10.1186/1471-2105-8-458.         Toggle abstract "Background: Coalescent simulations have proven very useful in many population genetics studies. In order to arrive to meaningful conclusions, it is important that these simulations resemble the process of molecular evolution as much as possible. To date, no single coalescent program is able to simulate codon sequences sampled from populations with recombination, migration and growth. Results: We introduce a new coalescent program, called Recodon, which is able to simulate samples of coding DNA sequences under complex scenarios in which several evolutionary forces can interact simultaneously (namely, recombination, migration and demography). The basic codon model implemented is an extension to the general time-reversible model of nucleotide substitution with a proportion of invariable sites and among-site rate variation. In addition, the program implements non-reversible processes and mixtures of different codon models. Conclusion: Recodon is a flexible tool for the simulation of coding DNA sequences under realistic evolutionary models. These simulations can be used to build parameter distributions for testing evolutionary hypotheses using experimental data. Recodon is written in C, can run in parallel, and is freely available from http://darwin.uvigo.es/. © 2007 Arenas and Posada; licensee BioMed Central Ltd."