BEAST is built on a large body of prior work and appropriate citations for individual modules, models and components will be listed when BEAST is run. BEAST-Users mailing list. Users are strongly advised to join the BEAST mailing-list. This will be used to announce new versions and advise users about bugs and problems.

To inform BEAUti/BEAST about the sampling dates of the sequences, go to the Tips menu and select the “Use tip dates” option. By default all the taxa are assumed to have a date of zero (i.e. the sequences are assumed to be sampled at the same time; BEAST considers the present or most recent sampling time as time 0).

FigTree is a program for viewing trees, including summary information produced by TreeAnnotator, and producing publication quality figures.

We have renamed the release that would have been called BEAST v1.10.5 as BEAST X v10.5.0. This is to distinguish it from the independent project called BEAST 2 – see: https://www.beast2.org. These projects have been running in parallel for many years which has restricted this BEAST project to using the v1 major release version and only ...

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.

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.

You will then run BEAST. Second Tutorial This tutorial follows directly on from the first, looking at the output of BEAST, diagnosing problems and summarising the results. This tutorial will introduce some of the utilities packaged with BEAST, logcombiner and treeannotator, as well as the external applications, Tracer and FigTree.

BEAST will often write numbers in scientific notation to maintain precision. Some software programs may have problems with this, so this option will convert these to decimal numbers. Renumber output states. If selected, this will renumber the output states to a sequential series. Resample states at lower frequency

Using BEAGLE with BEAST 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 …

Below is the BEAST DTA inference with all of the simulated outbreak cases (so 100% of the population has been sequenced and sampled in this case). References & Further Reading. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.