![]() ![]() BEAUti2 is provided as a part of the BEAST2 package so you do not need to install it separately. The screenshots used in this tutorial are taken on a Mac OS X computer however, both programs will have the same layout and functionality on both Windows and Linux. For us it simply means that the interface will be the same on all platforms. BEAUti2 - 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 TreesīEAST2 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. This will help the investigator determine which estimates of parameters can be trusted and which cannot. It is important to understand under which circumstances to use which model and when molecular calibration works. ![]() ![]() The molecular clock model aims to estimate the substitution rate of the data. In this tutorial we will explore how priors are selected and how molecular clock calibration works using H3N2 influenza A data from the flu virus spreading in the USA in 2009. It is not always easy to pick a proper model of tree generation (tree prior), substitution model, molecular clock model or the prior distribution for an unknown parameter. Specifying proper priors and starting values is crucial and can be a difficult exercise in the beginning. When priors are not specified correctly, it may cause runs to take a long time to converge, not converge at all or cause a bias in the inferred trees and model parameters. In the Bayesian analysis of sequence data, priors play an important role. ![]()
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