Cladistic analysis of genotype data-application to GAW15 Problem 3

Given the increasing size of modern genetic data sets and, in particular, the move towards genome-wide studies, there is merit in considering analyses that gain computational efficiency by being more heuristic in nature. With this in mind, we present results of cladistic analyses methods on the Genetic Analysis Workshop 15 Problem 3 simulated data (answers known). Our analysis attempts to capture similarities between individuals using a series of trees, and then looks for regions in which mutations on those trees can successfully explain a phenotype of interest. Existing varieties of such algorithms assume haplotypes are known, or have been inferred, an assumption that is often unrealistic for genome-wide data. We therefore present an extension of these methods that can successfully analyze genotype, rather than haplotype, data.