I have data for 5 individuals of 15 lineages (normalized gene expression, 75 total samples), a phylogeny, and would like to calculate the maximum likelihood under brownian motion, then compare the result to a model with selection (i.e. an Ornstein Uhlenbeck model) while retaining information about within species variation.
Does anyone know a program that could help me do this? Using EVE (Rohlfs et al. 2015), I'm able to calculate the likelihoods of the OU model, but not under brownian motion.