BEAUti - Bayesian Evolutionary Analysis UtilityīEAUti2 is a graphical user interface tool for generating BEAST2 XML configuration files.īoth BEAST2 and BEAUti2 are Java programs, which means that the exact same code runs on all platforms. This tutorial is written for BEAST v2.7.x (Bouckaert et al., 2014 Bouckaert et al., 2019). Programs used in this Exercise BEAST2 - Bayesian Evolutionary Analysis Sampling Trees 2īEAST2 ( ) is a free software package for Bayesian evolutionary analysis of molecular sequences using MCMC and strictly oriented toward inference using rooted, time-measured phylogenetic trees. Two other fundamental differences are the parameters that are inferred and the way sampling is treated. In the coalescent, time is modeled to move backwards, from the present to the past, while in the birth-death approach it is modeled to go forwards. The conceptual difference between the coalescent and birth-death approaches lies in the direction of the flow of time. ![]() The first one is the Coalescent Bayesian Skyline plot (Drummond et al., 2005), which is based on the coalescent model, and the second one is the Birth-Death Skyline plot (Stadler et al., 2013) based on the birth-death model. In this tutorial we will look at two different methods to infer these dynamics from sequence data. It is non-parametric since there is no underlying system of differential equations governing the inference of these dynamics. The so-called Skyline methods allow to extract this information from phylogenetic trees in a non-parametric manner. Population dynamics influence the shape of the tree and consequently, the shape of the tree contains some information about past population dynamics.
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