Summary Course notes and exercises for 'Molecular Epidemiology of Viruses in R'. Background Practice Prerequisites Resources Retrieving sequences Theory Practice Retrieving sequences example Retrieving annotations example Exercises Sequence alignment Theory Practice Nucleotide alignment Reverse alignment Exercise Distance-based analyses Theory Practice Clustering exercise Maximum likelihood based analyses Theory Practice Model choice exercise RAxML exercise Visualising trees Theory Practice * [ape exercise)(viz/exercise1.md) [ggtree exercise)(viz/exercise2.md) Time-stamped phylogenies Theory Practice Root-to-tip exercise Least squares dating exercise MrBayes exercise Effective population size estimation Theory Practice Fitting coalescent models Fitting birth-death models Tree shape Theory Practice Asymmetry exercise Structured populations Theory Practice 'Mugration' exercise colgem exercise Workflows An example analysis Discussion References