Interpreting the FLOCK algorithm from a statistical perspective

We show that the algorithm in the program FLOCK (Duchesne & Turgeon 2009) can be interpreted as an estimation procedure based on a model essentially identical to the STRUCTURE (Pritchard et al. 2000) model with no admixture and non-correlated allele frequency priors. Rather than using MCMC, the FLOCK algorithm searches for the maximum-a-posteriori estimate of this STRUCTURE model via a simulated annealing algorithm with a rapid cooling schedule (namely, the exponent on the objective function --> ∞). We demonstrate the similarities between the two programs in a two step approach. First, to enable rapid batch processing of many simulated data sets, we modified the source code of STRUCTURE to use the FLOCK algorithm, producing the program FLOCKTURE. With simulated data we confirmed that results obtained with FLOCK and FLOCKTURE are very similar (though ockture is some 200 times faster). Second, we simulated multiple large data sets under varying levels of population differentiation ...