**Important:** Times are in Central European Summer Time (UTC+2).

Monday | Tuesday | Wednesday | Thursday | Friday | |
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09:00 | Workshop Welcome |
Tanja Stadler Introduction to Phylodynamic Models (slides) |
Remco Bouckaert Language evolution and phylogeography (slides) |
Denise Kühnert Modelling epidemics with BEAST 2 (slides) |
Tim Vaughan Epidemic trajectory inference (slides) |

09:15 | Alexei Drummond Introduction to Bayesian Phylogenetics |
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10:45 | Morning Break | Morning Break | Morning Break | Morning Break | Morning Break |

11:15 |
First Steps in BEAST (lecture, tutorial) |
Fossilized Birth Death Model (tutorial) |
Language evolution (tutorial) |
Structured Birth-death Model (tutorial) |
StarBEAST 2 (tutorial) |

12:45 | Lunch Break | Lunch Break | Lunch Break | Lunch Break | Lunch Break |

13:30 | Icebreaker Games | TTB Pictionary | |||

14:00 | Substitution model averaging (tutorial) |
Bayesian Skyline Plot and Birth-death Skyline Plot (tutorial) |
LinguaPhy (tutorial) | The Structured Coalescent (lecture, tutorial) |
Inferring recombination graphs with BEAST 2 (lecture, tutorial) |

15:45 | Afternoon Break | Afternoon Break | Afternoon Break | Afternoon Break | Afternoon Break |

16:15 | Setting Priors (lecture) |
BEAST 2 Trouble-shooting (lecture) |
BEAST Clinic |
Understanding BEAST 2 XML (lecture) |
BEAST Clinic |

16:45 | Setting Priors (tutorial) |
BEAST 2 Trouble-shooting (tutorial) |
XML Hacking (tutorial) |
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18:00 | End of Day | Virtual Beers | End of Day |

Please ensure the following software is installed prior to the start of the workshop.

**Java 8 or higher:**This is required by BEAST 2 (download).**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 v2.6**for the workshop (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).**BEAGLE (optional):**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).**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).

We are aware that some of the workshop participants do not have a mathematical background and may have difficulty understanding some of the theory. The two links below can help to refresh the basic concepts, but are by no means meant to be comprehensive resources.

- Seeing Theory: This website gives a very brief, but pretty and easy to understand introduction to many of the fundamental concepts in statistics.
- Ziheng Yang's statistics primer: Gives a more in-depth introduction to the topic.

The books below are not all focused on BEAST or even Bayesian phylogenetics. However, each of the books contains at least one background chapter on the theory of molecular evolution, as well as more in-depth chapters on the models implemented in BEAST and BEAST 2. Most of the books also contain at least some discussion of Bayesian inference.

- Bayesian Evolutionary Analysis with BEAST,
*Alexei J. Drummond, Remco R. Bouckaert* - Molecular Evolution: A Statistical Approach,
*Ziheng Yang* - The Phylogenetic Handbook,
*Philippe Lemey, Marco Salemi, Anne-Mieke Vandamme* - Molecular Evolution: A Phylogenetic Approach,
*Roderick D.M. Page, Edward C. Holmes* - Inferring Phylogenies,
*Joseph Felsenstein*

In addition, the following review papers might be useful:

- Bayesian molecular clock dating of species divergences in the genomics era,
*Mario dos Reis, Phillip Donoghue, Ziheng Yang* - Evolutionary analysis of the dynamics of viral infectious disease,
*Oliver Pybus, Andrew Rambaut* - Bayesian molecular dating: opening up the black box,
*Lindell Bromham, Sebastián Duchêne, Xia Hua, Andrew M. Ritchie, David A. Duchêne, Simon Y. W. Ho*