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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 molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without ...
BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics package. It can make use of highly-parallel processors such as those in graphics processing units (GPUs) found in many PCs. The current version of BEAGLE will only work with BEAST v1.6 or later.
BEAST can be downloaded from the following link: BEAST X v10.5.0-beta5 - UNIX/Linux version 46.2MB; This will download a compressed tar archive (a ‘.tgz’ file).
First Tutorial. An introductory tutorial to getting started with BEAST. This tutorial describes the use of BEAUti and BEAST to analyse some primate sequences and estimate a phylogenetic tree. It will take you through the process of importing an alignment, making choices about the model, generating a BEAST XML file. You will then run BEAST.
Features. Cross-platform graphical tree display. Three different tree styles: rectangular, polar and radial. Display of node heights, branch lengths, support values and other annotations. Node height range bars if available. Collapse of clades into triangles. Colouring of branches and tip labels. Colouring by annotation (for example, support ...
Installing BEAST. BEAST has been developed in Java, which allows the same code to run on any platform that has the Java software installed. We have also created packages for each of the common operating systems to provide a user-interface that is ‘native’ and familiar.
BEAST offers a range of prior distributions to model population size changes through time (i.e., demography). These are coalescent priors, where the effective population size N e varies through time according to a certain function N e (t). Other, non-coalescent priors such as the Yule and birth-death processes are available in BEAST, but these ...
The aim of this tutorial is to estimate the ancestral locations of the virus using a Bayesian discrete phylogeographic approach and, at the same time, infer the history of host jumping using the same model approach. Using an extension of the discrete diffusion model, we will then test the factors that underly the host transition dynamics.
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 sequences have been collected at the same time) and dated-tip trees (where sequences have been collected at different dates). It is designed for ...
This tutorial describes the use of BEAUti and BEAST to analyse some primate sequences and estimate a phylogenetic tree. It will take you through the process of importing an alignment, making choices about the model, generating a BEAST XML file. You will then run BEAST. This tutorial follows directly on from the first, looking at the output of ...
