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 coala for
conduction the simulations.

coala

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.

scrm

The R package scrm contains is a version of the identically named coalescence
simulator for the evolution of biological sequences. It offers convenient
wrapper functions for calling the simulator, and transforms the simulation
results to a format that is easily usable from within R.

Other Software

scrm

The simulator scrm can generate genetic data that evolved
according to a given model. It implements an efficient
algorithms that operates both backwards-in-time and along the
sequence to generate a realistic correlation between
genetic positions. It is written in C++11.