Abstract
Infectious disease epidemiology makes use of mathematical models and molecular typing methods to probe pathogen transmission. Models and the basic reproductive number R(0) are a powerful tool for understanding disease dynamics and the impact of interventions, while genetic methods to characterize infectious agents give us an increasingly highly resolved picture of transmission over the short term of outbreaks, and the longer term of international spread. These two approaches are complementary, and are being combined in an approach termed ‘phylodynamics’ which aims to understand disease dynamics by the analysis of genetic data.