Introduction to BEAST2
This is a simple introductory tutorial to help you get started with using BEAST2 and its accomplices.
Jūlija Pečerska , Veronika Bošková and Louis du Plessis
Updated 9 Aug 2023 by laduplessis
Prior selection
Prior selection and clock calibration using Influenza A data.
Veronika Bošková , Venelin Mitov and Louis du Plessis
Updated 9 Aug 2023 by laduplessis
Troubleshooting convergence issues
Post-processing and improving performance
David A. Rasmussen
Updated 9 Aug 2023 by laduplessis
Troubleshooting initialization issues
Getting BEAST2 to start
Joëlle Barido-Sottani and Louis du Plessis
Updated 20 Jul 2023 by laduplessis
Skyline plots
Inference of past population dynamics using Bayesian Coalescent Skyline and Birth-Death Skyline plots.
Nicola F. Müller and Louis du Plessis
Updated 11 Jun 2024 by tgvaughan
Substitution model averaging
A tutorial using bModelTest
David A. Rasmussen , Carsten Magnus and Remco Bouckaert
Updated 24 Jul 2023 by laduplessis
Divergence Time Estimation
Dating Species Divergences with the Fossilized Birth-Death Process
Tracy A. Heath , Rachel Warnock and Bethany J. Allen
Updated 11 Aug 2023 by laduplessis
Bacter Tutorial
Inferring ARGs from bacterial sequence data.
Tim Vaughan
Updated 21 Jun 2018 by tgvaughan
StarBeast Tutorial
Estimating species tree from multilocus sequence data
Joseph Heled , Remco Bouckaert , Walter Xie , Alexei J. Drummond and Chi Zhang
Updated 2 Feb 2017 by laduplessis
Molecular dating using heterochronous data and substitution model averaging
Estimating the time of origin of the 2009 H1N1 pandemic in North America
Sebastian Duchene , Tim Vaughan and Veronika Boskova
Updated 5 Nov 2018 by tgvaughan
MASCOT v3.0.0 Tutorial
Parameter and State inference using the approximate structured coalescent
Nicola F. Müller
Updated 9 Jun 2023 by tgvaughan
Calibrated Species Trees
Estimating species divergence times using StarBEAST2
Huw A. Ogilvie
Updated 2 Feb 2017 by Unknown
Structured coalescent
Population structure using MultiTypeTree
Nicola F. Müller and Tim Vaughan
Updated 12 Jul 2017 by laduplessis
Structured birth death model
Population structure using the multi-type birth-death model
Denise Kühnert and Jūlija Pečerska
Updated 8 Jun 2023 by tgvaughan
The MSBD package
Inferring lineage-dependent birth and death rates
Joëlle Barido-Sottani
Updated 20 Jul 2023 by bjoelle
The ClaDS package
Inferring progressive changes in birth and death rates
Joëlle Barido-Sottani
Updated 18 Dec 2023 by Unknown
Species Trees and Species Delimitation with SNAPPER
Analyzing SNP or AFLP data
Adam Leaché and Remco Bouckaert
Updated 15 Apr 2024 by bjoelle
SCOTTI Tutorial
Transmission tree reconstruction with the structured coalescent
Louis du Plessis and Nicola de Maio
Updated 24 Jul 2017 by laduplessis
Model adequacy using BEAST2
Assessing clock and substitution models
David Duchêne
Updated 9 Feb 2017 by Unknown
StarBEAST2 v1.0.0 tutorial
Estimating species trees using StarBEAST2
Huw A. Ogilvie
Updated 15 Aug 2023 by Unknown
CladeAge Tutorial
Fossil-based divergence-time estimation with CladeAge
Michael Matschiner
Updated 21 Feb 2019 by mmatschiner
AIM in StarBeast2 v0.15.2 Tutorial
Inferring species trees and gene flow from multiple loci
Nicola F. Müller
Updated 14 Sep 2020 by nicfel
Model selection
Model selection with nested sampling
Remco Bouckaert
Updated 24 Mar 2019 by rbouckaert
Time stamped data
Time-stamped data
Remco Bouckaert , Walter Xie , Fábio K. Mendes and and Alexei Drummond
Updated 9 Jun 2024 by walterxie
Bayesian Skyline with adaptive parallel Tempering with CoupledMCMC Tutorial
Adaptive parallel Tempering
Nicola F. Müller
Updated 6 Dec 2019 by nicfel
Language Phylogenies
Using Babel to analyse linguistic data
Simon J. Greenhill and Konstantin Hoffmann
Updated 29 Jul 2019 by KonstantinHoffmann
Estimating Reassortment Networks with CoalRe
Estimating Reassortment Networks with CoalRe
Nicola F. Müller
Updated 1 Apr 2022 by tgvaughan
PIQMEE Tutorial
How to efficiently analyze large data sets containing duplicates
Veronika Bošková
Updated 28 Feb 2022 by boskovav
Skyline analyses for macroevolution
Estimating evolutionary parameters from species phylogenies
Bethany J. Allen
Updated 15 Mar 2023 by bethany-j-allen

If you found Taming the BEAST helpful in designing your research, please cite the following paper:

Joëlle Barido-Sottani, Veronika Bošková, Louis du Plessis, Denise Kühnert, Carsten Magnus, Venelin Mitov, Nicola F. Müller, Jūlija Pečerska, David A. Rasmussen, Chi Zhang, Alexei J. Drummond, Tracy A. Heath, Oliver G. Pybus, Timothy G. Vaughan, Tanja Stadler (2018). Taming the BEAST – A community teaching material resource for BEAST 2. Systematic Biology, 67(1), 170–-174. doi: 10.1093/sysbio/syx060