Contribution of genomic analysis to epidemiological studies of emerging infectious diseases. (a) Genomic analysis begins with obtaining a multiple sequence alignment of pathogen sequences from which a phylogeny can be built to represent the evolutionary relationship between samples. Further population genetic analysis using the coalescent framework can reveal the population history of the pathogen based on the sample phylogeny. (b) Coupling phylogeny with additional information is useful for uncovering zoonotic origins, the spatiotemporal patterns of disease spread, and transmission chains. The results of such phylogenetic analysis should be interpreted with care as the direction of transmission is not always clear and there might exist missing intermediate links. (c) Coalescent analysis of pathogen genealogy is used to characterize past epidemiological dynamics and estimate epidemiological parameters, such as the reproductive number.