Abstract
Next-generation sequencing (NGS) technology offers new opportunities for understanding the evolution and dynamics of viral populations within individual hosts over the course of infection. We review simple methods for estimating synonymous and nonsynonymous nucleotide diversity in viral genes from NGS data without the need for inferring linkage. We discuss the potential usefulness of these data for addressing questions of both practical and theoretical interest, including fundamental questions regarding the effective population sizes of within-host viral populations and the modes of natural selection acting on them.