Tutorial: Topology Weighting

By Simon Martin, 29 January 2020


  • Python 3+
  • R 3.0+
    • ape
    • data.table
  • Phyml (for part 2 only)

How to run this exercise

For this activity, you will need to connect to the Amazon instance both via a terminal and via RStudio. For the connection via terminal, you can either use a terminal program on your own computer and then connect using SSH (ssh [email protected]), or you can use the terminal that comes with Guacamole (ec2-XX-XXX-XX-XXX.compute-1.amazonaws.com:8080/guacamole/). Then navigate to the activity folder:
cd ~/workshop_materials/29_topology_weighting

To run R scripts and view pdf files produced with R, open an RStudio connection in your browser (ec2-XX-XXX-XX-XXX.compute-1.amazonaws.com:8787) and navigate to the directory ~/workshop_materials/29_topology_weighting.

Topology weighting activity

The activity is available on Simon Martin’s GitHub repository: Topology Weighting.

Topology weighting is a means to quantify relationships between taxa that are not necessarily monophyletic. The method is published in: Martin and Belleghem 2017.