Spring 2026

We will reproduce the phylogenetic analyses of Pervasive hybridizations in the history of wheat relatives by Glemin et al (2019).

Software

Week	Session	Topic	Pre-class work	Lecture notes	Homework
1	01/23	Introduction and reproducibility practices		notes	Set-up local folder for the class (HW)
2	01/30	Paper discussion	Read Glemin et al, 2019; Optional reading Marcussen et al, 2014
3	02/06	Goal of the analyses, required software and data		notes	Make sure all software is properly installed in your computer
4	02/13	Gene tree inference		notes	Run RAxML on all genes
5	02/20	Species tree: supermatrix (full concatenation)		notes	Finish the RAxML analyses on your own and visualize the results; Optional: run the script to concatenate genes yourself
6	02/27	Species tree: supermatrix (10Mb sliding window)		notes	Finish the RAxML analyses on your own and visualize the results; Optional: run the script to create the 10Mb windows yourself
7	03/06	Species tree: supertree and coalescent-based (new analysis)		notes	Finish the wASTRAL analyses
8	03/13	Species tree results (Figure 1)	Install and read about ggtree	notes
9	03/20	Species network inference (new analysis)		notes	Leave the snaq job running in the background
10	03/27	Hybrid tests: HyDe		notes	Leave HyDe analyses for 10Mb windows running in the background
	04/03	Spring break
11	04/10	HyDe visualizations (Figures 3-4)
12	04/17	Hybrid tests: MSCQuartets and visualizations		notes
13	04/24	Species network visualization (Figure 5)
14	05/01	Open question: other analyses
	05/04	Final reproducible script due

See list of topics, grading and academic policies in the syllabus