Viruses, as a population of subcellular entities of genetic material in a package, are at least an order of magnitude as numerous as that of their cellular hosts, on which they depend. While the particulars of the emergence of the ancestors of viruses are unknown, the evolutionary histories of their genes are possible by the evolutionary methods of gene sequence comparison and phylogenetic reconstruction. These studies depend on nucleotide or protein sequence data and a reference to the underlying process of genetic replication, which is a cause of taxon-specific differences in the rates of genetic mutation and correction of replication errors. Viral types also do not easily fit within the confines of traditional typologies, such as the use of a host preference for a biological marker of their taxonomic assignments. Instead, their population processes are dynamic and vary across taxa, which are causes of genetic change and new viral lineages. Since a naive deterministic model of evolution is not supported in the corpus of modern science, it is instead an ideal to infer knowledge of viral origins by models based on the stochastic processes of molecular evolution. These approaches are the basis for validating and building knowledge on virus evolution that leads to confidence and robustness in scientific findings (a requisite to the formation of a scientific belief).