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MRBAYES: Bayesian inference of phylogenetic trees [PDF]

Bioinformatics, 2001
Abstract Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
Fredrik Ronquist, John P Huelsenbeck, Ronquist Fredrik   +2 more
exaly   +3 more sources

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Parallel algorithms for Bayesian phylogenetic inference

Journal of Parallel and Distributed Computing, 2003
The combination of a Markov chain Monte Carlo (MCMC) method with likelihood-based assessment of phylogenies is becoming a popular alternative to direct likelihood optimization. However, MCMC, like maximum likelihood, is a computationally expensive method. To approximate the posterior distribution of phylogenies, a Markov chain is constructed, using the
Duncan A Buell, Xizhou Feng, Peter J Waddell   +2 more
exaly   +2 more sources

Empirical evaluation of a prior for Bayesian phylogenetic inference [PDF]

Philosophical Transactions of the Royal Society B: Biological Sciences, 2008
The Bayesian method of phylogenetic inference often produces high posterior probabilities (PPs) for trees or clades, even when the trees are clearly incorrect. The problem appears to be mainly due to large sizes of molecular datasets and to the large-sample properties of Bayesian model selection and its sensitivity to the prior ...
Ziheng Yang
exaly   +3 more sources

Variational Bayesian inference for association over phylogenetic trees for microorganisms

Journal of Applied Statistics, 2020
With the advance of next generation sequencing technologies, researchers now routinely obtain a collection of microbial sequences with complex phylogenetic relationships. It is often of interest to analyze the association between certain environmental factors and characteristics of the microbial collection.
Dong Wang, Kent Eskridge
exaly   +3 more sources

Bayesian inference of ancestral dates on bacterial phylogenetic trees [PDF]

Nucleic Acids Research, 2018
ABSTRACT The sequencing and comparative analysis of a collection of bacterial genomes from a single species or lineage of interest can lead to key insights into its evolution, ecology or epidemiology. The tool of choice for such a study is often to build a phylogenetic tree, and more specifically when possible a dated
Nicholas Croucher, Stephen Bentley, Daniel J Wilson   +2 more
exaly   +6 more sources

Sequential Bayesian Phylogenetic Inference

Systematic Biology
Abstract The ideal approach to Bayesian phylogenetic inference is to estimate all parameters of interest jointly in a single hierarchical model. However, this is often not feasible in practice due to the high computational cost. Instead, phylogenetic pipelines generally consist of sequential analyses, whereby a single point estimate from
Sebastian Höhna, Allison Y Hsiang
openaire   +2 more sources

A Bayesian Model of AFLP Marker Evolution and Phylogenetic Inference

Statistical Applications in Genetics and Molecular Biology, 2007
Amplified Fragment Length Polymorphism (AFLP) markers are formed by selective amplification of DNA fragments from digested total genomic DNA. The technique is popular because it is a relatively inexpensive way to produce large numbers of reproducible genetic markers.
Ruiyan, Luo, Andrew L, Hipp, Bret, Larget   +2 more
openaire   +2 more sources

Bayesian Inference in molecular Phylogenetics

2005
Abstract ‘l’he Bayesian method of statistical inference combines the prior for parameters with the data to generate the posterior distribution of parameters, upon which all inferences about the parameters are based. The method has become very popular due to recent advances in computational algorithms.
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Clock-constrained tree proposal operators in Bayesian phylogenetic inference

2008 8th IEEE International Conference on BioInformatics and BioEngineering, 2008
Bayesian Markov chain Monte Carlo (MCMC) has become one of the principle methods of performing inference of phylogenetic trees. The MCMC algorithm requires the definition of a transition kernel over the state space, which depends on tree proposal operators.
Sebastian Höhna, Michael Defoin-Platel, Alexei J. Drummond   +2 more
openaire   +1 more source