The study here focuses on influenza, although the techniques are readily applied to other rapidly evolving organisms. Influenza has three types, A, B and C, classified based on serological analysis. To date, only type A sequences have been demonstrably associated with global pandemics [4] . Since modern surveillance began in the 1930s, type B has only been responsible for mild epidemics while type C has been nearly asymptomatic in human infection. Several subtypes of A, notably H1N1 and H3N2, are currently co-circulating in the human population. As the H1N1 and H3N2 subtypes may be as divergent from each other as they are from types B and C, we will refer to all types and subtypes simply as subtypes for the remainder of this paper. We select for this study three genes, coding for hemagglutinin (HA), the matrix protein (MP) and the non-structural protein (NS) responsible for interfering with host immune response. Subtype C has a hemagglutinin-esterase gene that is analogous to the hemagglutin gene in other subtypes [1] . We hence refer to the hemagglutinin gene generally and the hemagglutininesterase gene when referring specifically to the subtype C sequences.