With the advent of sequencing, phylogenetic and phylodynamic methods proved to be invaluable in estimating key epidemiological parameters such as the basic reproductive number and the duration of the infectious period. Furthermore, these methods provide an estimate of the total infected population size, a quantity not easily measurable using classic epidemiological approaches. These methods were in particular applied to sequence data of the recent West Africa Ebola outbreak and the ongoing Zika epidemic in South America. Besides between-host dynamics, the tools are also capable of revealing within-host dynamics of chronic infections such as HIV or HCV. In my research I focus on development of phylodynamic methods capable of handling large datasets resulting from next-generation sequencing efforts, which contain many biological sequence duplicates, and evaluating which methods are most appropriate for sequence data being collected during epidemic spread.