Links
Some other programs for Bayesian estimation of phylogeny:
- BAli-Phy - Simultaneous Bayesian estimation of alignment and phylogeny (and other parameters).
- BEAST/BEAST2 - Bayesian Evolutionary Analysis by Sampling Trees. Strength in molecular clock analyses.
- BayesPhylogenies - Bayesian inference using mixed- and heterotachy models.
- ExaBayes - Software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters.
- PhyCas - Bayesian phylogenetic inference in Python (using polytomy priors, marginal likelihood estimation, and more).
- PhyloBayes - Phylogenetic reconstruction using infinite mixtures (CAT model).
- RevBayes - Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language.
Some tools for use with MrBayes:
- Burntrees - Tree- and parameter-file manipulations and format conversions.
- DensiTree - Program for qualitative analysis of sets of trees.
- FigTree - Interactive plotting of trees.
- PartitionFinder - Model selection of partitioned data (using Maximum Likelihood).
- PlotMCMCoutput - Quick plotting of MCMC output.
- RWTY - Plotting and analysing MCMC output (trees and parameter files).
- SumTrees - Tree file manipulations and format conversions.
- Tracer - Plotting and analysing MCMC output (parameter files).
- VMCMC - A graphical and statistical analysis tool for Markov chain Monte Carlo traces in Bayesian phylogeny.