The aim of this program is to allow users to simulate admixture with selection, but this program can also be used as a general purpose population simulator. The capabilities of this program include simulating realistic genetic architectures (recombination, chromosomal structure, realistic number of markers genome wide, linkage markers loci), complex selection including natural and sexual selection, frequency dependent selection, indirect genetic effects and demographic processes including migration and bottlenecks. A strength of this program is the ability to specify selection based on any mathematical operation, allowing flexibility without requiring user reprogramming.
If you use this program, please cite
Cui, R., Schumer, M., & Rosenthal, G. G. (2016). Admix’em: a flexible framework for forward-time simulations of hybrid populations with selection and mate choice. Bioinformatics, 32(7), 1103-1105.
Detailed manual is found on the wiki page of the github repository: https://github.com/melop/admixem/wiki.