Hierarchical clustering of essential viral entry proteins from the Ebola virus (Envelope glycoprotein), Influenza virus A (strain A, subtype H1N1) (Hemagglutinin), and Influenza virus B (strain B) (Glycoprotein NB) was performed in order to identify trends hidden among the subtle changes in the amino acid sequences of those proteins. The clustering provided clues as to how these viruses changed in the population. Clustering results revealed time-dependent and location-dependent patterns of organization. Furthermore, the temporal and geographical pattern shown in our clusters reinforces the idea that an evolutionary arms race is occurring at the viral-host protein interface. The patterns observed here may be used to better assess the novelty of future outbreaks and to gain a better understanding of virus proliferation through changing times and environments.