Msprime is a coalescent simulator and library for processing tree-based genetic data. Msprime can simulate the coalescent with recombination over whole chromosomes for hundreds of thousands of samples, and very efficiently process the resulting genealogies using tskit.
If you use msprime in your work, please cite the PLOS Computational
Biology paper.
See here for
full citation details.
Please see the documentation for further details.
Msprime is very portable, and provides a number of installation options. See here for details.