BEAST is a cross-platform program and fast, flexible software architecture for Bayesian analysis of molecular sequences using MCMC (Markov chain Monte Carlo). It is completely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

This package contains the BEAST program, BEAUti, TreeAnnotator and other utility programs.

The purpose behind the development of BEAST is to bring a large number of complementary evolutionary models (substitution models, insertion-deletion models, demographic models, tree shape priors, relaxed clock models, node calibration models) into a single coherent framework for evolutionary inference.

In a BEAST analysis, it is possible to allow each codon position to have a different substitution rate, a different amount of rate heterogeneity among sites, and a different amount of rate heterogeneity among branches, whilst sharing the same intrinsic ratio of transitions to transversions with the other codon positions.

In BEAST, divergence time estimation has also been extended to include relaxed phylogenetics models, in which the rate of evolution is allowed to vary among the branches of the tree.

Bayesian Markov chain Monte Carlo (MCMC) has already been enthusiastically embraced as the state-of-the-art method for phylogenetic reconstruction, largely driven by the rapid and widespread adoption of MrBayes. Firstly, Bayesian methods allow the relatively straightforward implementation of extremely complex evolutionary models. Secondly, there is an often erroneous perception that Bayesian estimation is "faster" than heuristic optimization based on a maximum likelihood criterion.

BEAST 2, is a latest version of BEAST is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.

The workflow is in the following ways:

Create an XML file using BEAUTi containing our data set and other information (i.e. model, MCMC settings). This file will be the input file of BEAST.

• Loading the NEXUS file

• Setting the dates of the taxa

• Setting the evolutionary model

• Setting the molecular clock model

• Setting the tree prior model

• Priors

• MCMC operators

• Setting the MCMC options

• Saving and Loading BEAUti files

• Setting the dates of the taxa

• Saving and Loading BEAUti files

• Generating the BEAST XML file

Features

• easy model specification

• encouragement of replication

• broad data compatibility and intelligent processing

• integration of expert knowledge

• it contains 81 packages

• provides models for DNA and protein sequence evolution

• highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data

• gives statistical alignment and a wide range of options for prior distributions

• attempts to minimize the time taken to evaluate a state by only recalculating the likelihood for parts of the model that have changed from the previous state.