The ability to simulate social contact networks, transmission networks, pathogen phylogenies, and pathogen genome sequences that capture a wide range of scenarios can enhance molecular epidemiology. However, the utility of such simulations depends entirely on their ability to capture important properties of the real-world epidemics they are used to study, which in turn depends on the appropriateness of the model assumptions behind the simulations. In this chapter, I introduce the FAVITES-Lite framework and discuss how one can use it to design and execute realistic epidemic simulations that appropriately model real-world epidemics of interest.