Parasites successfully exist within the host as a result of highly specific genetic adaptations. Therefore, detecting genes that contain relevant adaptive mutations can provide a guide to biological processes that are potentially essential to the parasite. Random genetic mutations that confer selective advantage can act to alter amino acids so as to confer gain of function that has positive impact on the survival of the parasite. Directional selection of advantageous mutations results from an elevated rate of nonsynonymous substitutions in rapidly evolving genes. Genes on which this positive selection operates are considered to have an evolutionary characteristic such that the normalized number of nonsynonymous (dn) substitutions is greater than that of synonymous (ds) substitutions. By searching in a statistically robust way for genes that contain this characteristic, it is possible to apply a stringent method to identify genes that may be under positive selection and thus to identify biological processes involving those genes that are essential to the survival of the parasite. Genes detected typically class into those under host immune surveillance and those intrinsic to pathways essential to survival of the parasite within the host. Depending on their function and location of protein expression, such genes have the potential to provide exceptional vaccine and drug candidates.