Optimist: Inference of positive selection
Optimist is a simple software package for inferring positive selection from marker dynamics in an asexual population.
Markers allow for the easy identification of subsets of a population in an evolutionary experiment. The spread of a beneficial mutation through a subset of the population leads to an increase in the frequency of a marker relative to the remainder of the population.
Our method uses marker frequencies, recorded over time, to infer the establishment times and fitnesses of beneficial mutations. The method is able to infer the presence of standing variation in the initial population, and is suitable for use in calculating the distribution of beneficial fitness effects in a population.