population history

Alexander DH, Novembre J & Lange K 2009 Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655-1664.

• structure takes a Bayesian approach and relies on a Markov chain Monte Carlo (MCMC) algorithm to sample the posterior distribution
• we use the same likelihood model but focus on maximizing the likelihood rather than on sampling the posterior
• high-dimensional optimization is much faster than high-dimensional MCMC
• our maximum likelihood approach can accommodate many more markers