Hybrid-Lambda is a software package that can simulate gene trees within a rooted species network or a rooted species tree under the Kingman’s coalescent or Lambda coalescent process.

Sha Zhu, James H Degnan, Sharyn J Goldstien, Bjarki Eldon. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. BMC Bioinformatics 2015, 16:292 doi: http://doi:10.1186/s12859-015-0721-y.

scrm simulates the evolution of genetic sequences. It takes a neutral evolutionary model as input, and generates random sequences that evolved under the model. As coalescent simulator, it traces the ancestry of the sampled sequences backwards in time and is therefore extremely efficient. Compared to other coalescent simulators, it can simulate chromosome-scale sequences without a measureable reduction of genetic linkage between different sites.

Paul R. Staab, Sha Zhu, Dirk Metzler and Gerton Lunter. scrm: efficiently simulating long sequences using the approximated coalescent with recombination. Bioinformatics (2015) 31 (10): 1680-1682. doi:10.1093/bioinformatics/btu861.