This protocol provides a method to study phage-bacteria interactions by generating a Network in Cytoscape using the application CoNet. To CoNet tutorial can help with analysis. Based on the methods from the following publication:Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15.