Tutorials

There are some general notes that apply to all tutorials. These tutorials use the graphical applications of BEAST to perform analyses using the provided example files:

• Divergence Dating (Version 2.2.0)
• Measurable evolving populations, estimating rates, bonus: BSP (Version 2.2.0)
• Extended Bayesian Skyline Plots
• STAR BEAST (Version 2.0.3)
• Ancestral reconstruction/Discrete phylogeography (Version 2.4.1)
• Continuous phylogeography on a sphere
• Birth Death Skyline (Version 2.1.1)
• Species delimitation with SNAPP tutorial (2018 version) •Species delimitation with SNAPPER (2021 version)
• Divergence-Time Estimation with SNP Data using SNAPPER
• Bayes Factor Delimitation of Species (*with genomic data; BFD*) (2018 Version)
• Divergence dating with sampled ancestors (FBD model)
• Beginner's Guide to the MultiTypeTree package for structured coalescent inference
• Codon Substitution Models Tutorial
• Phylodynamics using coalescent and birth-death models
• Phylodynamics using the birth-death SIR model
• Model selection with nested sampling
• Using the flexible BICEPS tree prior
• Using the flexible Yule skyline tree prior
• StarBeast3 efficient multi species coalescent

R tutorials

These tutorials use the R programming language to work with BEAST2.

• rOpenSci tutorial
• Tutorial at BES Methods
• many examples how to call BEAST2 from R, with BEAUti screenshots for comparison

Manuals

• A rough guide to SNAPP
• DensiTree
• MASTER documentation
• A Rough guide to CladeAge for fossil calibrations with BEAST

Taming the BEAST Tutorials

Additional tutorials are available from the Taming the BEAST website.

For developers

• Tutorial for Writing a BEAST2 package in Eclipse.
• Writing a package for a tree prior.

Video lectures

• Installing BEAST 2 and installing a package
• Cultural evolution
• Phylogeography part 1, part 2, part 3, part 4
• Model selection
• Model comparison
• Analysis with Snapper
• Species delimitation with SNPs using SNAPPER

How To's

• Fix starting tree
• Constraints Of Monophyly
• Plotting *BEAST tree
• DensiTree How To's
• Path Sampling
• Sample a discrete trait
• SNAPP for SNP and AFLP analysis
• EBSPAnalyser How To's
• Total evidence with FBD dating
• Coalescent SIR
• Morphological models
• Phylodynamic models
• Multi-gamma site models for dealing with heterotachy
• Fixing shift times in Birth-death Skyline model