Bayesian selection of continuous-time Markov chain evolutionary models.

By Marc A. Suchard, R. E. Weiss, Janet S. Sinsheimer. Molecular biology and evolution, 2001

821 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e7f8a69e00ea8601f1e05cdf226e94ca71e049ec

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Citations in the corpus

Estimating the timing of early eukaryotic diversification with multigene molecular clocks (2011, methodology): “If competing models converged in likelihood scores, the likelihoods were compared using Bayes factors (37) as assessed in Tracer, although we did not rely on this metric as the harmonic mean calculation of Bayes factors has been demonstrated to be unreliable (38).”
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space (2012, methodology): “It is standard practice today to select a substitution model for Bayesian phylogenetic inference using a priori model selection procedures (Goldman 1993; Posada 1998, 2008; Suchard et al. 2001).”
Population Demography and Genetic Diversity in the Pleistocene Cave Lion (2015, methodology): “…specifically, analyses were performed under a constant size population model and under relaxed demographic models (extended Bayesian skyline and GMRF Bayesian skyride) and the respective performance of the different models was assessed through the analysis of Bayes factors (Suchard et al., 2001).”
Evolutionary distance estimation under heterogeneous substitution pattern among lineages. (2002, positive): “It is a more general model than the Hasegawa, Kishino, and Yano (1985; HKY) model and is known to adequately describe patterns of DNA sequence evolution for many genes (e.g., Tamura 1994; Kumar 1996; Suchard, Weiss, and Sinsheimer 2001).”
Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales (2002, methodology): “Bayesian approaches have been used recently to test for a molecular clock (Suchard et al. 2001) and to estimate divergence times (under both strict and relaxed molecular clocks) (Thorne et al. 1998).”
Molecular phylogenetics of Myotis indicate familial-level divergence for the genus Cistugo (Chiroptera) (2010, methodology): “In the Bayesian framework Bayes factors (Kass and Raftery 1995; Newton and Raftery 1994; Suchard et al. 2001), as implemented in the program TRACER version 1.4 (Drummond and Rambaut 2003), were used to compare the relaxed uncorrelated exponential clock and relaxed uncorrelated lognormal clock.”
Bayesian analysis of elapsed times in continuous‐time Markov chains (2008, background): “Here, Yang and Rannala (2005) explore independent Exponential priors with two fixed rates, one for internal and one for external branches; while Suchard et al. (2001) introduce a hierarchical Exponential prior by simultaneously estimating the hyperprior rate.”
Bayesian Analysis of Correlated Evolution of Discrete Characters by Reversible‐Jump Markov Chain Monte Carlo (2006, background): “…in biology include choosing among models of gene sequence evolution (Boys and Henderson 2001; Huelsenbeck et al. 2004), testing among alternative phylogenetic topologies (Suchard et al. 2001; Lewis et al. 2005), and estimating demographic parameters in genealogical models (Opgen-Rhein et al. 2005).”
Bayesian Analysis of Molecular Evolution Using MrBayes (2005, methodology): “Here we will describe how Bayes factors can be used to choose among substitution models ([32]; also see [62]).”
Discovery of Seven Novel Mammalian and Avian Coronaviruses in the Genus Deltacoronavirus Supports Bat Coronaviruses as the Gene Source of Alphacoronavirus and Betacoronavirus and Avian Coronaviruses as the Gene Source of Gammacoronavirus and Deltacoronavirus (2012, methodology): “, a credible set that contains 95% of the sampled values) were calculated, and the best-fitting model was selected by a Bayes factor, using marginal likelihoods implemented in Tracer (see Table S1 in the supplemental material) (42).”
Computing Bayes factors using thermodynamic integration. (2006, methodology): “These methods are now applied extensively in molecular phylogenetics (Huelsenbeck and Ronquist, 2001; Larget and Simon, 1999; Lartillot and Philippe, 2004; Pagel and Meade, 2004; Suchard et al., 2001).”
Phylogeography takes a relaxed random walk in continuous space and time. (2010, background): “Fortunately, large differences , furnishing large BFs, are common when performing Bayesian model selection in a phylogenetic setting (Suchard et al. 2001; Edwards, Liu et al. 2007; Drummond and Suchard 2008) In borderline cases, more powerful BF estimators are readily available, for example, path…”
Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. (2004, methodology): “Suchard et al. (2001) showed how Bayes factors can be calculated for nested models using the Savage-Dickey ratio (Verdinelli and Wasserman, 1995).”