Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference

By Gautam Altekar, Sandhya Dwarkadas, John P. Huelsenbeck, Fredrik Ronquist. Bioinform., 2002

1,135 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Statistics and Probability

View Paper: https://www.semanticscholar.org/paper/d5d887304cf61ffb207aaaf84320fe1bafd0ef53

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

In Statistics and Probability

Citations in the corpus

Molecular Phylogeny of Owls (Strigiformes) Inferred from DNA Sequences of the Mitochondrial Cytochrome b and the Nuclear RAG-1 gene (2009, neutral): “(Ronquist & Huelsenbeck 2003, Altekar et al. 2004).”
Enabling future drug discovery by de novo design (2011, positive): “101 Their random sampling procedure is often coupled to the Metropolis criterion in order to facilitate escaping from lo-cal optima: 23 , 110 , 111 Structural changes that improve the score of a molecule are always accepted, whereas changes that decrease the score might be rejected [Eq.”
Computing Bayes factors using thermodynamic integration. (2006, background): “…= 1 to (cid:12) = 0 amounts to a warming-up, or melting of the MCMC. Note that the heated chains of the parallel Metropolis coupled Markov chains (Altekar et al., 2004) are de(cid:12)ned in a similar way (except that in there case, the posterior, rather than only the likelihood, is raised to the…”
A molecular phylogeny of the Odonata (Insecta) (2010, methodology): “Bayesian analysis was performed usingMRBAYES (version 3.1.2) (Huelsenbeck & Ronquist, 2001; Ronquist & Huelsenbeck, 2003; Altekar et al., 2004) with settings nst = 6, rates = invgamma and statefreqpr = dirichlet (1, 1, 1) for both partitions.”
ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era (2014, methodology): “Although the ML approach strives to optimize the likelihood of the tree and model given the data, Bayesian inference uses Markov chain Monte Carlo (MCMC) (Hastings 1970) sampling to integrate over the entire parameter space (e.g., model parameters and tree topologies) given the data and subjective p”
A Molecular Phylogeny of Santalaceae (Santalales) (2008, methodology): “Bayesian phylogenetic analyses were performed using the parallel Metropolis-coupled Markov chain Monte Carlo, or “p(MC)3,” algorithm in MrBayes version 3.1.2 (Ronquist and Huelsenbeck 2003; Altekar et al. 2004).”
Phylogeny of the leafhopper subfamily Deltocephalinae (Hemiptera: Cicadellidae) based on molecular and morphological data with a revised family‐group classification (2010, methodology): “1.2 (Huelsenbeck & Ronquist, 2001; Ronquist & Huelsenbeck, 2003) and with a parallel version (Altekar et al., 2004) run on a supercomputing cluster available through the National Center for Supercomputing Applications at University of Illinois at Urbana-Champaign.”
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space (2012, background): “MrBayes 3.2 does not support multithreading, but it does implement the message passing interface (MPI) for efficient parallel processing across large computer clusters (Altekar et al. 2004).”
Major clades of Agaricales: a multilocus phylogenetic overview (2006, methodology): “All datasets were analyzed with parallel and single-processor versions of MrBayes 3.1.1 (Altekar et al 2004, Ronquist and Huelsenbeck 2003).”
Identifying the sister group to the bees: a molecular phylogeny of Aculeata with an emphasis on the superfamily Apoidea (2012, methodology): “Bayesian analyses were performed using Parallel Mr Bayes v. 3.1.2 (Huelsenbeck & Ronquist 2001; Ronquist & Huelsenbeck 2003; Altekar et al. 2004).”
Reconstructing the Anomalodesmata (Mollusca: Bivalvia): morphology and molecules (2006, methodology): “MRBAYES 3.0 (Huelsenbeck & Ronquist, 2001; Altekar et al., 2004; for parallel implementation) was used for Bayesian inference under the GTR + I + Γ model, with three million generations for four chains starting from random trees, sampling every 100th tree.”
The taxonomy of the Caloplaca citrina group (Teloschistaceae) in the Black Sea region; with contributions to the cryptic species concept in lichenology (2009, methodology): “Bayesian phylogenetic analysis was carried out with a Metropolis-coupled Markov chain Monte Carlo (MCMCMC) algorithm (Altekar et al. 2004) implemented in MrBayes 3.0 (Ronquist and Huelsenbeck 2003).”