Despite the fact that bacteriophages are extremely active players in the global ecosystem, as well as the most abundant biological entities on the planet, much remains unknown about how these viruses function in their natural environments. Advances in full-genome sequencing technologies have generated a large collection of hundreds of genomes, which allows deep insight into their genetic evolution, and metagenomics technologies seem to promise more rewarding glimpses into their lifecycles and community structures. Previously we developed an automated approach to assemble a novel collection of orthologous gene families in phages, which gives us a powerful tool to study these fascinating organisms, and recently we have doubled its size and expanded its scope. Using this resource, we found that more than half of all gene families in phages are not shared with their cellular hosts, making them ideal candidates for diagnostic tests as sensitive and precise markers of specific viral families. Studies of the evolutionary processes of phages also have implications for their use as therapeutic agents, as well as expanding their role as tools for biotechnology and other applications. I will present a network analysis of genes shared between various groups of phages, as well as a procedure to identify such diagnostic marker genes. Together, these approaches reveal potential for bacteriophage taxonomy schemes that use genomic information rather than purely structural characteristics.