StarBEAST2 is a Bayesian implementation of the multispecies coalescent (MSC) that jointly infers gene and species trees directly from multiple sequence alignments. Trees inferred using this method contain not only topological relationships, but also estimates of species divergences times and gene coalescence times. Such trees are therefore often described as time trees.
This tutorial walks through through how to set up three kinds of species tree analyses using StarBEAST2. The first is basic species tree reconstruction using a strict nuclear clock rate. The second is a relaxed clock analysis where a separate molecular clock rate is estimated for each species branch. The third is a total evidence analysis where the times and rates and jointly estimated by integrating fossil data into the model.
If you found Taming the BEAST helpful in designing your research, please cite the following paper:
Joëlle Barido-Sottani, Veronika Bošková, Louis du Plessis, Denise Kühnert, Carsten Magnus, Venelin Mitov, Nicola F. Müller, Jūlija Pečerska, David A. Rasmussen, Chi Zhang, Alexei J. Drummond, Tracy A. Heath, Oliver G. Pybus, Timothy G. Vaughan, Tanja Stadler (2018). Taming the BEAST – A community teaching material resource for BEAST 2. Systematic Biology, 67(1), 170–-174. doi: 10.1093/sysbio/syx060