Developing tools for making inferences from genomic data

Abstract

The central question that the King lab seeks to answer is, "What happens on the genomic level when phenotypes evolve?" To this end, the core focus of my work has been on developing software and analytical methods that facilitate the ability of other researchers working in this space to answer their questions of interest. ... In the second chapter, we describe the problem of inferring ancestral haplotype frequencies from pooled sequence data. We discuss five approaches to this problem that have already been developed, and we discuss a new genetic algorithm based approach that we designed. We perform a benchmarking test on a method developed by Burke et al. and we compare that method to the genetic algorithm by evaluating the performance of each on a simulated dataset. We find that the new method outperforms the existing one.