OKEE Workshop - Hands-on Phylogenetics in R

4th Jan. 2023, ETHZ, Switzerland

Workshop Programme

1. Introductions to the basics of phylogenetics and the main concepts
2. How phylogenies are encoded in files on our computer, and how R ‘sees’ them
3. A brief overview on how to get a tree (published phylogenies, treebase, OTL, building from GenBank, …)
4. Get your tree in R: General checks (plotting, stats, monophyly)
5. Methods I: Phylogenetic signal
   • Continuous Traits
   • Discrete Traits
6. Methods II: Trait Evolution
   • Trait Models and Model testing
   • Ancestral State Reconstruction

Materials

Below the slides and code files used during the workshop. If you have questions or feedback feel free to contact me.

Slides

R-Code

R-Code Trait Evolution (Bonus material we didn’t get around to)

Data

Example-Tree

SterolTaxa