RNA viruses rapidly evade the host immune responses by changing targeted proteins. I will discuss how deep sequencing of HIV populations from many consecutive samples can be used to track virus evolution and quantify competing tendencies of immune escape and rapid replication. In a similar manner, the rapid evolution of influenza viruses necessitates the frequent updates of the seasonal influenza vaccines. We have used models of rapidly evolving populations to predict which strains of influenza virus are most likely to dominate future influenza seasons. Such models can inform the selection of virus strains used to produce influenza vaccines.