The more general aim of this tutorial is to: date of the most recent common ancestor of the sampled virus sequences.phylogenetic relationships with measures of internal node heights.The aim of this tutorial is to obtain estimates for the: We use the hemagglutinin (HA) gene of the H3N2 strain spreading across America alongside the pandemic H1N1 virus in 2009 (CDC, 2009/2010). In this tutorial, we will estimate the rate of evolution from a set of virus sequences that have been isolated either at one point in time (homochronous data) or at different points in time (heterochronous or time-stamped data). Practical: H3N2 flu dynamics - Heterochronous data It can interpret the node-annotations created on the summary trees by TreeAnnotator, allowing the user to display node-based statistics (e.g. FigTreeįigTree ( ) is a program for viewing trees and producing publication-quality figures. It can also be used to investigate potential parameter correlations. It helps to quickly view median estimates and 95% highest posterior density intervals of the parameters, and calculates the effective sample sizes (ESS) of parameters. This program can be used for visual inspection and to assess convergence. Tracer ( ) is used to summarize the posterior estimates of the various parameters sampled by the Markov Chain. TreeAnnotator is provided as a part of the BEAST2 package so you do not need to install it separately. It can also be used to summarise and visualise the posterior estimates of other tree parameters (e.g. ![]() TreeAnnotator is used to summarise the posterior sample of trees to produce a maximum clade credibility tree. 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 v2.5.2 (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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