BEAUti, BEAST and other programs
Rates and Dates
Temporal Signal using TempEst
Online phylodynamic inference
Phylodynamics of an epidemic
Phylodynamics of seasonal influenza
Analysing Continuous Traits
Create taxon sets
Specify sampling dates
Tip date sampling
Construct a model in BEAUti
Analyse BEAST output
Convergence diagnostics in Tracer
Create custom substitution models
Hierarchical Phylogenetic Model Tutorial
Markov Jumps and Rewards Tutorial
Adaptive MCMC Tutorial
Model Selection Tutorial
Model Selection Advanced Tutorial
Model Selection Examples
Clock Model Averaging Tutorial
Epoch Model Tutorial
Time-Dependent Rate Model Tutorial
Estimating Rates and Dates
Evolutionary Dynamics of Influenza
Model Selection and Testing
Phylogeographic Diffusion in Discrete Space
Phylogeographic Diffusion in Continuous Space, YFV
Phylogeographic Diffusion in Continuous Space, WNV
Effective Sample Size
BEAUti & The BEAST and other programs
Software packages in the BEAST family.
Click on the icons for more details.
Programs distributed as part of the core BEAST package
| Bayesian Evolutionary Analysis Utility. This program is used to import data, design the analysis, and generate the BEAST control file.
| Bayesian Evolutionary Analysis Sampling Trees. This is the main program that takes a control file generated by BEAUti and performs the analysis.
| This is a post-analysis program that will produce a summary tree from the output of BEAST.
| This is a utility program that will combine log files from different runs and reduce the sampling frequency (thin them).
| This is a utility program that will parse through a set of trees and extract statistics and information from them.
These programs are distributed independently but are important part of the BEAST toolkit.
| This is a graphical program for exploring the output of BEAST, diagnosing problems, and summarizing the results.
| This is a graphical program for viewing trees, displaying summary information from TreeAnnotator and generating publication-ready figures.
These programs that will be useful for specific types of data and analysis.
| A package for analysis and visualisation of pathogen pylodynamic reconstructions.
| This is a graphical program for looking for temporal signal in trees generated from tipdated sequences.
| This is a program for simulating sequence data under some of the same models implemented in BEAST.