MLSpeciationGenomics 2025

Workshops

The meeting includes three workshops including practical exercises. Below we include links to the material that will be used.

Software

Before the course starts, please install the following software on your own computer:

• Access to Unix system
• A good text editor, such as Sublime Text, NotePad++, Atom, BBEdit, TextEdit, vim, or emacs. Word is not a good text editor!
• Python. We will be using Jupyter Notebooks
• Python libraries for the machine learning workshops: numpy, pandas, scikit-learn, tensorflow, and matplotlib
• R or RStudio with the package Rcpp
• For installing software: Conda and git (likely to be already provided by through your linux distribution) </br>

Parts

• Museums Genomics
  ↘Workshop 1. Museomics
  

• Experimental Evolution
  ↘Workshop 2. Detecting Targets of Selection in Experimental Evolution
  This workshop uses Bait-ER. You can find instructions on how to install the software here
  

• Machine Learning
  ↘Workshop 3. Machine learning topics in sequence analyses
  Please download the data and install the environments from the following links.
  ↘https://github.com/cmayer/ML-course_Iris-dataset-Dense-NN
  ↘https://github.com/KulyaNikita/Machine-Learning-Phylogenomics-Workshop-St-Andrews
  ↘https://github.com/parsec3/Machine-Learning-for-Alignments-and-Phylogenomics-Workshop-St-Andrews
  Please install python environment specified in the environment-ML-St-Andrews.yml file, e.g. using
  conda env create -f environment-ML-St-Andrews.yml
  ↘Workshop 4. PhyloDeep Project
  Please download ↘Workshop 4 materials here
  

• PoMoBalance
  For this workshop, we will be using the development RevBayes branch, where the polymorphism-aware models are all available. Make sure you follow these instructions to install RevBayes. Please do not use conda to install RevBayes.
  ↘Workshop 5. PoMo Balance and RevBayes
  We will also need:
  
• Tracer
• FigTree