Spring 2026
We will reproduce the phylogenetic analyses of Pervasive hybridizations in the history of wheat relatives by Glemin et al (2019).
Software
- RAxML
- SuperTriplets
- ASTRAL
- Julia
- SNaQ
- PhyloPlots
- HyDe
- R
- ape, phangorn, ggtree, MSCQuartets
Schedule 2026
| Session | Topic | Pre-class work | Lecture notes | Homework |
|---|---|---|---|---|
| 01/23 | Introduction and reproducibility practices | notes | Set-up local folder for the class (HW) | |
| 01/30 | Paper discussion | Read Glemin et al, 2019; Optional reading Marcussen et al, 2014 | ||
| 02/06 | Goal of the analyses, required software and data | notes | Make sure all software is properly installed in your computer | |
| 02/13 | Gene tree inference | notes | Run RAxML on all genes | |
| 02/20 | Species tree: supermatrix (full concatenation) | notes | ||
| 02/27 | Species tree: supermatrix (10Mb sliding window) | notes | ||
| 03/06 | Species tree: supertree | |||
| 03/13 | Species tree: coalescent-based (new analysis) | |||
| 03/20 | Species tree results (Figure 1) | |||
| 03/27 | Species network inference (new analysis) | |||
| 04/03 | Spring break | |||
| 04/10 | Hybrid tests: HyDe | |||
| 04/17 | Hybrid tests: MSCQuartets (new analysis) | |||
| 04/24 | Species network (Figure 5) and hybridization results (Figures 3-4) | |||
| 05/01 | Open question: other analyses | |||
| 05/04 | Final reproducible script due |
More details
See list of topics, grading and academic policies in the syllabus