|
MrBayes is a program for Bayesian inference and model choice across
a wide range of phylogenetic and evolutionary models. MrBayes uses Markov
chain Monte Carlo (MCMC) methods to estimate the posterior distribution
of model parameters.
Program features include:
- A common command-line interface across Macintosh, Windows, and UNIX
operating systems;
- Extensive help available from the command line;
- Analysis of nucleotide, amino acid, restriction site, and
morphological data;
- Mixing of data types, such as molecular and morphological characters,
in a single analysis;
- Easy linking and unlinking of parameters across data partitions;
- An abundance of evolutionary models, including 4x4, doublet,
and codon models for nucleotide data and many of the standard
rate matrices for amino acid data;
- Estimation of positively selected sites in a fully hierarchical
Bayesian framework;
- Full integration of the BEST algorithms for the multi-species coalescent.
- Support for complex combinations of positive, negative, and backbone
constraints on topologies;
- Model jumping across the GTR model space and across fixed rate
matrices for amino acid data;
- Monitoring of convergence during the analysis, and access to a
wide range of convergence diagnostics tools after the analysis has finished;
- Rich summaries of posterior samples of branch and node parameters printed
to majority rule consensus trees in FigTree format;
- Implementation of the stepping-stone method for accurate estimation of
model likelihoods for Bayesian model choice using Bayes factors;
- The ability to spread jobs over a cluster of computers using MPI
(for Macintosh (OS X) and UNIX environments only);
- Support for the BEAGLE library, resulting in dramatic speedups for
codon and amino acid models on compatible hardware (NVIDIA graphics
cards);
- Checkpointing across all models, allowing the user to seemlessly
extend a previous analysis or recover from a system crash;
|
