Please visit the workshop page for information about the venue, travel and the workshop committee.
Programme
In case GitHub is not accessible and tutorial files cannot be downloaded, all of the tutorials for this workshop are mirrored on GitLab.
| Invited talks | Lectures | Tutorials | Interactive |
| Sunday 2025/07/13 |
Monday 2025/07/14 |
Tuesday 2025/07/15 |
Wednesday 2025/07/16 |
Thursday 2025/07/17 |
Friday 2025/07/18 |
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|---|---|---|---|---|---|---|
| 08:45 | Arrival | Welcome | Housekeeping | Housekeeping | Housekeeping | Housekeeping |
| 09:00 | Joëlle Barido-Sottani Introduction to Bayesian phylogenetics |
Simon Ho Phylogenetics and molecular dating in the genomic era (link) |
Sasha Gavryushkina Birth-death models for estimating speciation and epidemiological parameters (link) |
Xing Xu Morphology-based phylogenetic analysis: Taxon sampling, character formulation and coding (link) |
Arong Luo Molecular data and their use in macroevolutionary studies (link) |
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| 09:15 | ||||||
| 09:30 | ||||||
| 09:45 | ||||||
| 10:00 | Break | Break | Break | Break | Break | |
| 10:15 | Chi Zhang First steps in BEAST2 and setting priors |
Walter Xie LinguaPhylo and LPhyBEAST |
Rachel Warnock Divergence time estimation and total evidence dating |
Joëlle Barido-Sottani Structured models in phylodynamics |
Sophie Seidel Single-cell phylogenetics for developmental biology |
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| 10:30 | ||||||
| 10:45 | ||||||
| 11:00 | ||||||
| 11:15 | Introduction to BEAST2 (tutorial) |
Analysing Time-Stamped Data with LinguaPhylo and BEAST (tutorial) |
Dating species divergences with the fossilized birth-death process (tutorial) |
Modelling macro-evolution with BDMM-prime (tutorial) |
Estimating single-cell trees from lineage tracing data with TiDeTree (tutorial) |
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| 11:30 | ||||||
| 11:45 | Visualizing BEAST2 results in R (optional tutorial) |
Modelling pathogen spread with MASCOT (optional tutorial) |
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| 12:00 | ||||||
| 12:15 | Lunch IVPP |
Lunch IVPP |
Free afternoon | Lunch IVPP |
Lunch IVPP |
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| 12:30 | ||||||
| 12:45 | ||||||
| 13:00 | ||||||
| 13:15 | Joëlle Barido-Sottani Molecular clock models |
Rong Zhang Inference using continuous traits |
Chi Zhang Species tree inference and the multispecies coalescent |
Rachel Warnock Morphological models and total-evidence dating |
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| 13:30 | ||||||
| 13:45 | Molecular clock dating and modelling rate variation (tutorial) |
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| 14:00 | Registration IVPP (main building) |
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| 14:15 | Modelling continuous trait evolution in BEAST2 (tutorial) |
Estimating species trees using StarBEAST3 (tutorial) |
Modelling morphological evolution in BEAST2 (tutorial) |
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| 14:30 | Prior selection and clock calibration (optional tutorial) |
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| 14:45 | ||||||
| 15:00 | ||||||
| 15:15 | Break | Break | Break | Break | ||
| 15:30 | Chi Zhang Tree priors |
Joëlle Barido-Sottani Troubleshooting & practical tips |
Robert Yuan Model selection via marginal likelihood estimation |
Free Q&A session and wrap-up (optional) |
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| 15:45 | ||||||
| 16:00 | ||||||
| 16:15 | ||||||
| 16:30 | Inference of past population dynamics using skyline models (BEAST2 tutorial ,LPhyBEAST tutorial) |
BEAST2 initialization (tutorial) |
Model selection with nested sampling (tutorial) |
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| 16:45 | ||||||
| 17:00 | BEAST2 convergence (optional tutorial) |
Departure | ||||
| 17:15 | ||||||
| 17:30 | BEAST Clinic & Tutorial catch-up (optional) |
BEAST Clinic & Tutorial catch-up (optional) |
BEAST Clinic & Tutorial catch-up (optional) |
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| 17:45 | ||||||
| 18:00 | Dinner IVPP (conference room) |
Dinner IVPP (conference room) |
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| 18:15 | ||||||
| 18:30 | Gala dinner Xiyuan dining room (Xiyuan hotel 2nd floor) |
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| 18:45 | ||||||
| 19:00 | Opening event IVPP (main building) |
Lecture slides
Slides to lectures are available from GitHub and mirrored on GitLab (in case GitHub is not accessible).
Required software
Please ensure the following software is installed prior to the start of the workshop.
- BEAST 2: BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. We will be using this software to perform analyses on the data brought to the workshop. We will be using BEAST v2.7 for the workshop (download). If you want to use the latest release of BEAST 2 you can upgrade the downloaded version to BEAST v2.7.8 by updating Beast.Base from the Package Manager in BEAUti. The developers would appreciate in any feedback you have about the new version!
- BEAGLE (optional, but strongly recommended): BEAGLE is a high-performance library that can perform the core calculations in BEAST2 (and many other phylogenetics packages) much faster. BEAGLE isn’t necessary for the workshop, but it will speed up your analyses (download).
- FigTree: FigTree is a graphical viewer of phylogenetic trees, specifically designed to display summarised and annotated trees produced by BEAST (download).
- Tracer: Tracer is a program for analysing the trace files generated by Bayesian MCMC runs. It can be used to check mixing, ESS, parameter correlations, etc. (download).
- Java: The official BEAST 2 releases come bundled with Zulu Java 17 and don’t need a separate Java installation anymore. However, FigTree and Tracer still require a Java Runtime Environment (JRE) to be installed. If you don’t have a suitable version of Java already installed, you can install Zulu Java 17 from Azul Systems. (download).
- LPhy Studio: We will be using LinguaPhylo for a tutorial. Please see the installation instructions on the website. You will also need to install the LPhyBEAST package in BEAST 2.
- R: R is a free software environment that provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering) and graphical techniques, and is highly extensible (download).
- RStudio (optional): RStudio provides a friendly front-end for R (download).
BEAST 2 packages
As with the software above, it is highly recommended to pre-install all of the BEAST2 packages we will be using over the course of the week. We will be using the following packages:
- BDMM-Prime
- BDSKY
- BEAST_CLASSIC
- BEASTLabs
- bModelTest
- CCD
- ClaDS
- contraband
- Mascot
- MM
- MSBD
- NS
- SA
- starbeast3
- TiDeTree
- TreeStat2
Additional resources
There are a lot of great resources for brushing up or deepening your knowledge of the models used in BEAST2. This is a selection of resources that we consider especially useful, several of which are freely available on the internet. It is not expected that you’ve worked through any of these before the workshop!
Phylogenetics and phylodynamics
- Paul Lewis’ Phyloseminar Phylogenetics 101 primer is an excellent introduction to the topic (4 hours of content):
- Decoding Genomes: From Sequences to Phylodynamics, Tanja Stadler, Carsten Magnus, Timothy Vaughan, Joëlle Barido-Sottani, Veronika Bošková, Jana S. Huisman, Jūlija Pečerska (PDF available free of charge from the website)
- Bayesian Evolutionary Analysis with BEAST, Alexei J. Drummond, Remco R. Bouckaert
- Molecular Evolution: A Statistical Approach, Ziheng Yang
- Inferring Phylogenies, Joseph Felsenstein
Statistics and Bayesian inference
- Information Theory, Inference and Learning Algorithms, David MacKay (PDF available free of charge from the website)
- Ziheng Yang’s statistics primer gives a short overview of the topic (excluding Bayesian inference).
- Richard McElreath’s Statistical Rethinking course uses Bayesian inference to teach data analysis.
Questions
Please contact the organizing committee at ttb.beijing@ivpp.ac.cn.
