Search Results - "Bouckaert, Remco R."

DensiTree: making sense of sets of phylogenetic trees by BOUCKAERT, Remco R

“…Motivation: Bayesian analysis through programs like BEAST (Drummond and Rumbaut, 2007) and MrBayes (Huelsenbeck et al., 2001) provides a powerful method for…”
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StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates by Ogilvie, Huw A, Bouckaert, Remco R, Drummond, Alexei J

“…Fully Bayesian multispecies coalescent (MSC) methods like *BEAST estimate species trees from multiple sequence alignments. Today thousands of genes can be…”
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Model Selection and Parameter Inference in Phylogenetics Using Nested Sampling by Russel, Patricio Maturana, Brewer, Brendon J., Klaere, Steffen, Bouckaert, Remco R.

“…Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high…”
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Variational Bayesian phylogenies through matrix representation of tree space by Bouckaert, Remco R

“…In this article, we study the distance matrix as a representation of a phylogeny by way of hierarchical clustering. By defining a multivariate normal…”
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bModelTest: Bayesian phylogenetic site model averaging and model comparison by Bouckaert, Remco R, Drummond, Alexei J

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OBAMA: OBAMA for Bayesian amino-acid model averaging by Bouckaert, Remco R

“…Bayesian analyses offer many benefits for phylogenetic, and have been popular for analysis of amino acid alignments. It is necessary to specify a substitution…”
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The origin and expansion of Pama–Nyungan languages across Australia by Bouckaert, Remco R., Bowern, Claire, Atkinson, Quentin D.

“…It remains a mystery how Pama–Nyungan, the world’s largest hunter-gatherer language family, came to dominate the Australian continent. Some argue that social…”
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Adaptive Metropolis-coupled MCMC for BEAST 2 by Müller, Nicola F., Bouckaert, Remco R.

“…With ever more complex models used to study evolutionary patterns, approaches that facilitate efficient inference under such models are needed…”
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An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference by Bouckaert, Remco R

“…We present a two-headed approach called Bayesian Integrated Coalescent Epoch PlotS (BICEPS) for efficient inference of coalescent epoch models. Firstly, we…”
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Detecting contact in language trees: a Bayesian phylogenetic model with horizontal transfer by Neureiter, Nico, Ranacher, Peter, Efrat-Kowalsky, Nour, Kaiping, Gereon A., Weibel, Robert, Widmer, Paul, Bouckaert, Remco R.

“…Abstract Phylogenetic trees are a central tool for studying language evolution and have wide implications for understanding cultural evolution as a whole. For…”
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bModelTest: Bayesian phylogenetic site model averaging and model comparison by Bouckaert, Remco R, Drummond, Alexei J

“…Reconstructing phylogenies through Bayesian methods has many benefits, which include providing a mathematically sound framework, providing realistic estimates…”
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Looking for trees in the forest: summary tree from posterior samples by Heled, Joseph, Bouckaert, Remco R

“…Bayesian phylogenetic analysis generates a set of trees which are often condensed into a single tree representing the whole set. Many methods exist for…”
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Species Delimitation using Genome-Wide SNP Data by Leaché, Adam D., Fujita, Matthew K., Minin, Vladimir N., Bouckaert, Remco R.

“…The multispecies coalescent has provided important progress for evolutionary inferences, including increasing the statistical rigor and objectivity of…”
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Racing algorithms for conditional independence inference by Bouckaert, Remco R., Studený, Milan

“…In this article, we consider the computational aspects of deciding whether a conditional independence statement t is implied by a list of conditional…”
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On Chain Graph Models for Description of Conditional Independence Structures by Studeny, Milan, Bouckaert, Remco R.

“…A chain graph (CG) is a graph admitting both directed and undirected edges with (partially) directed cycles forbidden. It generalizes both the concept of…”
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A comparison of methods for estimating prediction intervals in NIR spectroscopy: Size matters by Bouckaert, Remco R., Frank, Eibe, Holmes, Geoffrey, Fletcher, Dale

“…In this article we demonstrate that, when evaluating a method for determining prediction intervals, interval size matters more than coverage because the latter…”
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Optimizing Causal Orderings for Generating DAGs from Data by Bouckaert, Remco R

“…An algorithm for generating the structure of a directed acyclic graph from data using the notion of causal input lists is presented. The algorithm manipulates…”
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Properties of Bayesian Belief Network Learning Algorithms by Bouckaert, Remco R

“…Bayesian belief network learning algorithms have three basic components: a measure of a network structure and a database, a search heuristic that chooses…”
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A Stratified Simulation Scheme for Inference in Bayesian Belief Networks by Bouckaert, Remco R

“…Simulation schemes for probabilistic inference in Bayesian belief networks offer many advantages over exact algorithms; for example, these schemes have a…”
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On characterizing Inclusion of Bayesian Networks by Kocka, Tomas, Bouckaert, Remco R, Studeny, Milan

“…Every directed acyclic graph (DAG) over a finite non-empty set of variables (= nodes) N induces an independence model over N, which is a list of conditional…”
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