MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
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Summary
The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly, and provides more output options than previously, including samples of ancestral states, site rates, site dN/dS rations, branch rates, and node dates.
- Type
- article
- Published
- 2012-02-22
- Cited by
- 26,077
- References
- 33
- Access
- Open access
- OpenAlex
- https://openalex.org/W2148698435
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:16088459
Keywords
Markov chain Monte Carlo, Computer science, Tree (set theory), Speedup, Marginal likelihood
References
- Approximate Bayesian-inference With the Weighted Likelihood Bootstrap
- A compound poisson process for relaxing the molecular clock.
- Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.
- Phylogenetic Inference for Binary Data on Dendograms Using Markov Chain Monte Carlo
- On incomplete sampling under birth-death models and connections to the sampling-based coalescent.
- The conditioned reconstructed process.
- Examples of Adaptive MCMC
- Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods
- MODELTEST: testing the model of DNA substitution
- Bayesian selection of continuous-time Markov chain evolutionary models.
- Relaxed Phylogenetics and Dating with Confidence
- Computing Bayes factors using thermodynamic integration.
- High-resolution species trees without concatenation
- Divergence time and evolutionary rate estimation with multilocus data.
- A general comparison of relaxed molecular clock models.
- Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
- Improving marginal likelihood estimation for Bayesian phylogenetic model selection.
- jModelTest: phylogenetic model averaging.
- Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions.
- Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo.
Cited by
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- Eight independent nuclear genes support monophyly of the plovers: the role of mutational variance in gene trees.
- A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa
- The salmonid myostatin gene family: a novel model for investigating mechanisms that influence duplicate gene fate
- Identification of a Bacteria-Like Ferrochelatase in Strongyloides venezuelensis, an Animal Parasitic Nematode
- Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies.
- The Rediscovery of a Long Described Species Reveals Additional Complexity in Speciation Patterns of Poeciliid Fishes in Sulfide Springs
- Biogeography and host‐related factors trump parasite life history: limited congruence among the genetic structures of specific ectoparasitic lice and their rodent hosts
- Molecular Evolution of Vertebrate Neurotrophins: Co-Option of the Highly Conserved Nerve Growth Factor Gene into the Advanced Snake Venom Arsenalf
- Molecular evidence revealed Lepus hainanus and L. peguensis have a conspecific relationship
- Phylogeny of the Rhizobium-Allorhizobium-Agrobacterium clade supports the delineation of Neorhizobium gen. nov.
- Alike but different: the evolution of the Tubifex tubifex species complex (Annelida, Clitellata) through polyploidization
- Substrate Specificity of the Lanthipeptide Peptidase ElxP and the Oxidoreductase ElxO
- The fossilized birth–death process for coherent calibration of divergence-time estimates
- Molecular identification of Taenia mustelae cysts in subterranean rodent plateau zokors (Eospalax baileyi).
- DNA Barcoding of Bemisia tabaci Complex (Hemiptera: Aleyrodidae) Reveals Southerly Expansion of the Dominant Whitefly Species on Cotton in Pakistan
- A new quadrannulate species of Orobdella (Hirudinida, Arhynchobdellida, Orobdellidae) from central Honshu, Japan
- Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula
- Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences
- Evolution of pigment‐dispersing factor neuropeptides in panarthropoda: Insights from onychophora (velvet worms) and tardigrada (water bears)
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