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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 These samples are correlated because each sample is generated by a small perturbation of the previous sample. If you haven’t already, download and install beast following these instructions.

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Details about the individual programs that make up the beast package can be found here An mcmc analysis generates a series of samples from the posterior distribution This is a list of some of the models and features in beast:

For instructions on installing beast for a unix command line see this page

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 | bayesian evolutionary analysis sampling trees This is the main program that takes a control file generated by beauti and performs the analysis. Introduction genomic epidemiology combines classical epidemiological methods with genome sequence data to track and monitor both endemic pathogens and the emergence and spread of novel pathogens

In this tutorial, we will follow an outbreak through different phases and use phylogenetic methods to answer questions pertinent to understanding and controlling the outbreak In most applications of beast the prior is either uniform or a coalescent prior on the tree shape Sampling sampling is the main function of an mcmc run