Taming the BEAST - Tutorials

Species Trees and Species Delimitation with SNAPPER

Thu, 06 Nov 2025 10:58:31 +0000

Analyzing SNP or AFLP data
By Adam Leaché and Remco Bouckaert

Updated on 6 Nov 2025 by bjoelle : added PDF

Level: Intermediate
Requires: BEAST v2.7.x

Total Evidence Tutorial

Wed, 27 Aug 2025 12:34:33 +0000

Inferring phylogenies using genetic sequences and morphological characters
By Bethany J. Allen and Joëlle Barido-Sottani

Updated on 27 Aug 2025 by Unknown : fixes

Level: Intermediate
Requires: BEAST v2.7.7

Structured coalescent

Mon, 11 Aug 2025 10:06:34 +0000

Population structure using MultiTypeTree
By Nicola F. Müller and Tim Vaughan

Updated on 11 Aug 2025 by jugne : Merge pull request #3 from jugne/master Updated TtB tutorial to work with BEAUti template upgrade

Level: Professional
Requires: BEAST v2.7.x

BDMM Prime for Macroevolution

Thu, 17 Jul 2025 05:44:51 +0000

The fossilized birth-death process and extensions
By Rachel C. M. Warnock , Timothy G. Vaughan and Louis du Plessis

Updated on 17 Jul 2025 by rachelwarnock : Merge pull request #4 from laduplessis/master Fix liquid error and two other tiny changes

Level: Intermediate
Requires: BEAST v2.7.7

StarBeast3 Tutorial

Wed, 16 Jul 2025 19:07:47 +0000

Estimating species trees using StarBeast3
By Ugne Stolz and Jordan Douglas

Updated on 16 Jul 2025 by laduplessis : Move files in precooked_runs so they appear on website

Level: Intermediate
Requires: BEAST v2.7.8

TiDeTree Tutorial

Tue, 15 Jul 2025 12:58:09 +0000

Reconstructing time-scaled single-cell phylogenies from genetic lineage tracing data
By Sophie Seidel

Updated on 15 Jul 2025 by laduplessis : Update figure file names

Level: Intermediate
Requires: BEAST v>= 2.7

Divergence Time Estimation

Sun, 13 Jul 2025 14:47:15 +0000

Dating Species Divergences with the Fossilized Birth-Death Process
By Tracy A. Heath , Rachel Warnock and Bethany J. Allen

Updated on 13 Jul 2025 by laduplessis : Add pdf for the pdf tutorial (temporary fix while latex can't build) and re-add the extant bears pdf figure (needed for pdf tutorial)

Level: Intermediate
Requires: BEAST v2.7.x

Troubleshooting initialization issues

Sun, 13 Jul 2025 14:24:30 +0000

Getting BEAST2 to start
By Joëlle Barido-Sottani and Louis du Plessis

Updated on 13 Jul 2025 by laduplessis : Update to reflect that online docs are updated to BEAST 2.7.8 and also some other small edits

Level: Beginner
Requires: BEAST v2.7.x

Prior selection

Fri, 11 Jul 2025 22:10:24 +0000

Prior selection and clock calibration using Influenza A data.
By Veronika Bošková , Venelin Mitov and Louis du Plessis

Updated on 11 Jul 2025 by jugne : Figure update

Level: Beginner
Requires: BEAST v2.7.x

Molecular clock dating and modelling rate variation

Fri, 11 Jul 2025 09:59:40 +0000

Accounting for evolutionary rate variation in passerine birds
By Simon Ho and Jacqueline Nguyen

Updated on 11 Jul 2025 by laduplessis : Fix typo Logcomineeeeer

Level: Beginner
Requires: BEAST v2.7.7

Model selection

Thu, 10 Jul 2025 15:22:33 +0000

Model selection with nested sampling
By Remco Bouckaert

Updated on 10 Jul 2025 by jugne : Fixed some typos

Level: Intermediate
Requires: BEAST v2.7.x

Introduction to BEAST2

Tue, 08 Jul 2025 09:07:01 +0000

This is a simple introductory tutorial to help you get started with using BEAST2 and its accomplices.
By Jūlija Pečerska , Veronika Bošková and Louis du Plessis

Updated on 8 Jul 2025 by jugne : Update README.md

Level: Beginner
Requires: BEAST v2.7.x

Time stamped data

Thu, 03 Jul 2025 05:11:41 +0000

Time-stamped data
By Remco Bouckaert , Walter Xie , Fábio K. Mendes and Eva Li and Alexei Drummond

Updated on 3 Jul 2025 by walterxie : relative rates

Level: Beginner
Requires: BEAST v2.7.8

The ClaDS package

Thu, 19 Jun 2025 13:10:53 +0000

Inferring progressive changes in birth and death rates
By Joëlle Barido-Sottani

Updated on 19 Jun 2025 by Unknown : updated XML and priors

Level: Intermediate
Requires: BEAST v2.7.x

The MSBD package

Thu, 19 Jun 2025 12:00:54 +0000

Inferring lineage-dependent birth and death rates
By Joëlle Barido-Sottani

Updated on 19 Jun 2025 by Unknown : modified starting tree setup

Level: Intermediate
Requires: BEAST v2.7.x

Structured birth death model

Wed, 04 Jun 2025 09:23:45 +0000

Population structure using the multi-type birth-death model
By Denise Kühnert and Jūlija Pečerska

Updated on 4 Jun 2025 by tgvaughan : Fixed typo.

Level: Professional
Requires: BEAST v2.7.4

MASCOT v3.0.0 Tutorial

Mon, 02 Jun 2025 17:51:38 +0000

Parameter and State inference using the approximate structured coalescent
By Nicola F. Müller

Updated on 2 Jun 2025 by jugne : Revert bullet points

Level: Intermediate
Requires: BEAST v2.7.x

Visualizing BEAST2 results in R

Fri, 23 May 2025 15:59:22 +0000

Tutorial on visualising results from BEAST2 analyses.
By Cecilia Valenzuela Agüí and Ugnė Stolz

Updated on 23 May 2025 by jugne : Update master-refs.bib

Level: Intermediate
Requires: BEAST v2.7.x

Troubleshooting convergence issues

Mon, 14 Apr 2025 11:27:22 +0000

Post-processing and improving performance
By David A. Rasmussen

Updated on 14 Apr 2025 by bjoelle : added figures and files for starting tree section

Level: Beginner
Requires: BEAST v2.7.x

Skyline plots

Tue, 11 Jun 2024 08:22:24 +0000

Inference of past population dynamics using Bayesian Coalescent Skyline and Birth-Death Skyline plots.
By Nicola F. Müller and Louis du Plessis

Updated on 11 Jun 2024 by tgvaughan : Corrected typo.

Level: Beginner
Requires: BEAST v2.7.x

StarBEAST2 v1.0.0 tutorial

Tue, 15 Aug 2023 17:40:53 +0000

Estimating species trees using StarBEAST2
By Huw A. Ogilvie

Updated on 15 Aug 2023 by Unknown : Merge pull request #1 from laduplessis/master Update to BEAST 2.7

Level: Intermediate
Requires: BEAST v2.7.x

Substitution model averaging

Mon, 24 Jul 2023 12:37:34 +0000

A tutorial using bModelTest
By David A. Rasmussen , Carsten Magnus and Remco Bouckaert

Updated on 24 Jul 2023 by laduplessis : Merge pull request #1 from bjoelle/master updated for 2.7

Level: Intermediate
Requires: BEAST v2.7.x

Skyline analyses for macroevolution

Wed, 15 Mar 2023 11:17:43 +0000

Estimating evolutionary parameters from species phylogenies
By Bethany J. Allen

Updated on 15 Mar 2023 by bethany-j-allen : Remove citation section

Level: Professional
Requires: BEAST v2.6.6

Estimating Reassortment Networks with CoalRe

Fri, 01 Apr 2022 12:50:24 +0000

Estimating Reassortment Networks with CoalRe
By Nicola F. Müller

Updated on 1 Apr 2022 by tgvaughan : Merge pull request #2 from tgvaughan/patch Removed non-matching HA and NA sequences (both from Helsinki)

Level: Intermediate
Requires: BEAST v2.6.0

PIQMEE Tutorial

Mon, 28 Feb 2022 14:15:49 +0000

How to efficiently analyze large data sets containing duplicates
By Veronika Bošková

Updated on 28 Feb 2022 by boskovav : Merge pull request #1 from tgvaughan/patch-1 Removed references to tutorial template bib file.

Level: Intermediate
Requires: BEAST v2.6.3