How to prepare for the workshop

The basics

As the workshop heavily relies on UNIX and VCF-files, you can find introductory tutorials below:

  • Basic UNIX tutorial: Evomics unix tutorial
    On the first day of the workshop, you can join the workshop team for a UNIX Primer (optional).
  • VCF-file tutorial: First steps in genomic data analysis
    A basic tutorial on the first steps in population genomic data analyses: exploring the Variant Call Format (VCF), quality filtering, and Principal Component Analysis (PCA). We taught this exercise in 2019 and 2020 but had mixed feedback since many participants were already familiar with these analyses. In 2022, we therefore removed it from the schedule. Should you have no prior experience with VCF files and basic VCF-file analyses, please have a look at this tutorial and just drop Julia an email to request the example data and the plotting script.


General background reading

If during your preparation or in the workshop you find the wish to have additional background theory or refresh your knowledge on population genetics theory, there is the following online resource on general population genetics, with R code examples:


Additional reading

For the interested: you can find below, per topic, reviews and articles suggested by the faculty and workshop team (don’t worry about reading everything):

Bayesian inference

Easy-to-follow visual explanations of likelihood and Bayesian inference can be found in Paul Lewis’ phyloseminars available on Youtube:


Natural selection / adaptation

Two reviews on the identification of signals of selection:

A guide to landscape genomics:


Genome-wide genealogy inference

The paper on Relate by Speidel et al. and a commentary by Kelley Harris:


The multi-species coalescent

A review on the model and a paper on tree discordance:


Measuring divergence and gene flow between species

Examples of genome-wide analyses of speciation and gene flow, using Heliconius butterflies as a model system:


Structural Variation

Reviews providing frameworks to study SVs:

Examples of SV analyses in mammals and birds:


Machine Learning

Review introducing machine learning and how it can be used in population genetics:


Simulation inference

Publication describing the model behind msprime and use cases: