In this era of genomic epidemiology there have been high hopes that sequencing will reveal who infected whom in a way that is not accessible with standard epidemiological investigations. To this end, several methods have been developed. This course will describe some of these, and compare and contrast their assumptions and data requirements. The student will learn to use several of them to reconstruct transmission – who infected whom – in densely sampled outbreaks with the help of pathogen sequence data.