MrBayes 3: Bayesian phylogenetic inference under mixed models
MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models to analyze heterogeneous data sets and explore a wide variety of structured models mixing partition-unique and shared parameters.
MRBAYES: Bayesian inference of phylogenetic trees
The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo, and an executable is available at http://brahms.rochester.edu/software.html.
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
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.
Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.
Dispersal-Vicariance Analysis: A New Approach to the Quantification of Historical Biogeography
- F. Ronquist
- Environmental Science
- 1 March 1997
This work presents a new biogeographic method, dispersal-vicariance analysis, which reconstructs the ancestral distributions in a given phylogeny without any prior assumptions about the form of area relationships, and describes the algorithms that find the optimal reconstruction.
Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
The proposed parallel algorithm retains the ability to explore multiple peaks in the posterior distribution of trees while maintaining a fast execution time, and performance results indicate nearly linear speed improvement in both programming models for small and large data sets.
Bayesian phylogenetic analysis of combined data.
A Bayesian MCMC approach to the analysis of combined data sets was developed and its utility in inferring relationships among gall wasps based on data from morphology and four genes was explored, supporting the utility of morphological data in multigene analyses.
A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera
- F. Ronquist, S. Klopfstein, L. Vilhelmsen, Susanne Schulmeister, D. Murray, A. Rasnitsyn
- Geography, Environmental ScienceSystematic Biology
- 26 July 2012
The results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic.