Evolutionary analysis of short read sequences

Next-generation sequences (NGS) returns a large collection of short-read fragments.  If these fragments come from a mixed sample of different genomes, it is challenging to reconstruct the evolutionary history of these genomes. This project will extend a method that we have developed in our laboratory that simultaneously infers the constituent haplotypes, phylogeny, and evolutionary parameters of the individuals in the sample. The method is a computational Bayesian method that relies on the use of Markov chain Monte Carlo.