This document gives a brief guide to the practicalities of performing an MCMC analysis with the BEAST software package, by going through a number of examples in detail.
These archives contain complete practicals to using BEAST, Tracer and FigTree complete with the required data sets.
correct a mistake in v1.2: missing prior of node calibration (HomiCerco).
Estimating a date of divergence using fossil calibration for primates.
Estimating a date of divergence using a host co-divergence for feline papillomaviruses (similar to the primate practical but virus-orientated).
Estimating the rate of evolution from serially-sampled sequences (dated tips) using an RSVA (human respiratory syncytial virus subgroup A) data set.
A three-part virus practical that covers the same material as the two above but has an additional part on Bayesian Skyline Plots.
A two-part practical focused on human influenza virus A (A/H1N1pdm and A/H3N2).
Describes the use of the BEAUti GUI application to create a BEAST XML file for analysing data where sequences have known dates of sampling.
Describes the use of the Tracer GUI application to analyse the output of BEAST.
Describes the use of the TreeAnnotator utility and FigTree to summarize the trees produced by BEAST.
This tutorial has yet to be written.
This tutorial describes the use of BEAUti and BEAST to analyse some primate sequences and estimate the date of divergence of humans and chimps when the mutation rate is known.
A short list of techniques for increasing the effective sample size (ESS) for a BEAST analysis.
The following tutorials describe how to edit BEAST XML format to create more advanced analyses. Many of these option can now be selected within BEAUti making these tutorials obselete. However, we have left these for reference purposes and to learn more about the XML format.
Describes how to create and log various statistics in order to estimate posterior distributions of particular hypotheses of interest.
Describes using the BEAST XML format to place an upper limit on the age of the root of the tree.
Describes how to specify a uniform bounded or parametrically distributed prior on the age of the MRCA of a subset of taxa.
Describes editing the BEAST XML input file to provide an initial user-specified tree for the MCMC to start with.
Describes editing the BEAST XML input file to create a UPGMA tree for the MCMC to start with.
Describes editing the BEAST XML input file to constrain a particular group of taxa to be kept monophyletic throughout the analysis. This can be used to keep an outgroup as the outgroup.
Describes editing the BEAST XML to add an additional data partition with a different substitution model and rate.
Describes how to place a probability distribution as a prior on the age of the root of the tree or the substitution rate.
Describes how to incorporate multiple unlinked loci into a single analysis.
Describes how to create a general data type for a custom type of discrete characters. (Updated on 22/01/2010)
Describes how to set up time-reversible nucleotide models other than HKY and GTR.
Describes how to alter a BEAST XML file so that BEAST only samples from the Prior distribution.
Reconstructing ancestral states/sequences
Describes how to reconstruct an ancestral state or sequence at a particular node
Describes how to perform model selection in BEAST using the harmonic mean estimator (HME), a posterior simulation-based analogue of Akaike's information criteration (AICM), path sampling (PS) and stepping-stone sampling (SS). This tutorial replaces the previous model comparison tutorial.
This tutorial describes how to extend standard XML documents, such as generated by BEAUTi, to include analysis under time-heterogenous (epoch) models of substitution (see Bielejec et al., 2014).
Describes how to set up a demographic model involving two epochs and a transition time.
Describes how to set up an upper limit on population size in a Bayesian Skyline Plot.
This short practical explains how to set up an Extended Bayesian Skyline Plot (EBSP) analysis in BEAST, and how to generate some EBSP plots.
This tutorial describes how to setup an analysis of continuous traits to look at the correlation between them in a phylogenetically corrected way (i.e., the comparative method). This examples uses some mitochondrial sequence data to sample trees whilst jointly estimating the coevolution of 5 continuous morphological traits.
These tutorials describe how to set up the analyses described in Lemey, Rambaut, Drummond & Suchard (2009) PLoS Comput Biol.
Describes how to edit a BEAST XML file to set up a discrete phylogeographic analysis using a standard continuous-time Markov chain.
Describes how to modify a discrete phylogeographic model XML file to set up BSSVS.
Describes how to annotate an MCC tree using the modal location states.
Describes how to convert a location-annotated MCC to KML for visualization in Google Earth.
Describes how to identify rates that are frequently invoked to explain the diffusion process and how to visualize these in Google Earth.
These tutorials describe how to set up the analyses described in Lemey, Rambaut, Welch & Suchard (2010) MBE.
Describes how to edit a BEAST XML file to set up a phylogeographic analysis in continuous space using a standard random walk.
Describes how to modify an XML file that specifies a homogenous Brownian diffusion phylogeographic model to set up a relaxed random walk.
These tutorials will describe how to set up HPMs in BEAST as described in Suchard, Kitchen, Sinsheimer & Weiss (2003) Syst Biol
Describes how to edit a BEAST XML file to set up a hierarchical phylogenetic model across several evolutionary parameters.
The objective of this tutorial is to estimate the species tree that is most probably given the multi-individual multi-locus sequence data. The species tree has 9 taxa, whereas each gene tree has 26 taxa. *BEAST will co-estimate three gene trees embedded in a shared species tree (see Heled and Drummond, 2010 for details).