The overall aim of this research is to better understand the evolutionary associations among retroviruses and their host species. Retroviruses, such as HIV in humans, must become part of the host cell’s genome to produce new viruses. When a germline cell is infected there is a chance for the retrovirus to be passed on to the host’s offspring as an inherited endogenous retrovirus (ERV). Consequently, retroviruses have colonized host genomes as ERVs for millions of years, and thereby providing a remarkable record of past virus activity that is utilized for studying the biology and evolution of virus-host relationships. Here we develop and apply new methods to identify and characterize ERVs across diverse host genomes, utilizing data that has been produced in large-scale sequencing projects. We study retrovirus evolution along host species phylogeny and evaluate effects of retroviruses and ERVs on host genomic variation as well as contributions to host biology and phenotypic evolution.