A Novel Algorithm for Adaptive and Neutral Evolutionary Patterns Associated with HIV Drug Resistance

This paper presents the development and application of a novel algorithm for the detection and classification of the adaptive and neutral evolutionary patterns associated with HIV drug resistance. Here, the Bayesian theorem will be used to predict the prevalence of an evolutionary pattern over a population to determine the class of its behaviour, whether it arose predominantly from neutral evolution, positive selection or negative selection. As an illustration, we will explain the algorithmic procedure in an application to real data, focusing on two- and three-mutation patterns that confer resistance to a drug agent.