SNaQ Tutorial: from alignments to phylogenetic network
This website has an alternative tutorial for SNaQ to the one in the PhyloNetworks wiki. Here, we use a Docker for the installation of Dependencies and we use a real dataset (baobabs) to illustrate the pipeline from multilocus alignments to phylogenetic network.
These learning materials were created as part of the workshop in the Kew Royal Botanical Gardens: Methodological Advances in Reticulate Evolution taught in November 2023 co-organized with George Tiley, Ziheng Yang and Tomas Flouri.
Learning outcomes
By the end of the tutorial, you will be able to
- estimate gene trees (and posterior distributions) from multilocus alignments with MrBayes
- estimate concordance factors from the estimated posterior distributions with BUCKy
- estimate a phylogenetic network from the estimated concordance factors with SNaQ
Schedule
| Topic | Lecture notes | Time |
|---|---|---|
| 1. Theory: Estimating phylogenetic networks from multilocus alignments | theory | 13:00 - 15:00 |
| Break | 15:00 - 15:30 | |
| 2. Set up: dependencies and data | set-up, data | 15:30 - 16:30 |
| 3. From alignments to concordance factors with the TICR pipeline | TICR | 16:30 - 17:30 |
| Q&A | 15:30 - 16:00 |
| Topic | Lecture notes | Time |
|---|---|---|
| 4. Estimating a phylogenetic network with SNaQ | SNaQ | 9:00 - 10:30 |
| Break | 10:30 - 11:00 | |
| 5. Comparative models for trait evolution on networks | traits | 11:00 - 12:00 |
Citations
If you use the TICR pipeline, PhyloNetworks and/or SNaQ for your work, please cite the references in here
Meet the instructor
Claudia Solís-Lemus is an assistant professor at the Wisconsin Institute for Discovery and the Department of Plant Pathology at the University of Wisconsin-Madison. Originally from Mexico City, she did her Undergraduate degrees in Actuarial Sciences and Applied Mathematics at ITAM. Then, she did a MA in Mathematics and a PhD in Statistics at the University of Wisconsin-Madison.
