GeneEvolve is a user-friendly, fast, and memory efficient forward-time simulator of realistic whole-genome sequence and SNP data. It is described in this publication. It can handle complex evolutionary scenarios and generates individual-level phenotypes and realistic whole-genome sequence or SNP data. GeneEvolve runs forward-in-time, which allows it to provide a wide range of scenarios for mating systems, selection, population size and structure, migration, recombination, and environmental effects. The software is maintained on github and can be downloaded here.
I highly recommend reading the Manual and running the example scripts included before trying to use it. Questions about the program can be sent to Rasool Tahmasbi (firstname.lastname@example.org).
The new version of GeneEvolve supplants an older (unpublished) version of GeneEvolve that was written in R - that can still be downloaded from here, but is no longer maintained.