BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed …

Running BEAST for the first time This tutorial will guide you through running BEAST and some of its accessory programs to do a simple phylogenetic analysis. If you haven’t already, download and …

BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed …

Tracer (now at version 1.7.2) is a software package for visualising and analysing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, …

Running BEAUti Running BEAST Analyzing the BEAST output using Tracer Summarizing and visualizing the trees Visualizing MCC trees and calculating Bayes factor support for rates using …

TreeAnnotator is a program to summarize the information from a sample of trees produced by BEAST onto a single “target” tree. The summary information includes the posterior probabilities of the nodes …

The BEAUti & The BEAST software package Bayesian Evolutionary Analysis Utility (BEAUti) BEAUti is a graphical user-interface (GUI) application for generating BEAST XML files. It is distributed in the …

LogCombiner allows you to combine log and tree files from multiple independent runs of BEAST. It can be run with a user-interface or as a command-line utility.

TempEst (formerly known as ‘Path-O-Gen’) is a tool for investigating the temporal signal and ‘clocklikeness’ of molecular phylogenies. It can read and analyse contemporaneous trees (where all …

BEASTGen can also be used to create BEAST XML files (as its name suggests). A template can be based on a BEAST XML file and be used to ‘insert’ data from another data file to create a file ready …