SNaQ Tutorial: from alignments to phylogenetic network
This website has an alternative tutorial for SNaQ to the one in the PhyloUtilities website. Here, we provide an alternative (optional) set-up using a Docker for the installation of dependencies and we use a real dataset (baobabs) to illustrate the pipeline from multilocus alignments to phylogenetic network.
Version 1.0 of this tutorial was taught as part of the workshop in the Kew Royal Botanical Gardens: Methodological Advances in Reticulate Evolution (November 2023) co-organized with George Tiley, Ziheng Yang and Tomas Flouri.
The current version of this tutorial will be taught at the Molecular Evolution Workshop (MOLE) in the Marine Biology Lab at Woods Hole, MA (June 2025).
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
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.
