Jaatha is a parameter estimation method for estimating parameters of
evolutionary models from genetic data. It applies machine learning
to simulated data to generate a model with is then in turn used
to estimate composite-likelihood parameters for the biological
data. It is implemented as an
R package and uses
conduction the simulations.
Coala is an
R framework for coalescent simulation. It can
be used to specify and simulated biological models of
evolution. The models are build in a modular approach, and
coala automatically calls different existing coalescent
simulators and parse their results. It is the most sophisticated
R package I have written so far.