AlleleRetain is a package implemented in R to simulate small populations. Output includes demographic trends and information, probability of retaining a rare allele, and accumulation of inbreeding over the simulated period. AlleleRetain also implements R package pedigree (available at http://cran.r-project.org/) to assess the simulated pedigrees and inbreeding coefficients.
AlleleRetain was developed and is maintained by Emily Weiser (visit my website here), with portions drawn from code originally written by Murray Efford (R package mohuasim; Animal Conservation 14:439-446). It is available on CRAN (cran.r-project.org) and has been used in a number of real-world management applications.
If you encounter problems while using AlleleRetain, please first consult the user guide (available on the Download page, and included with the package installation) and the R help manual included with the package. If you are still stuck or if you've found a bug in the program, inquiries may be sent here. I will try to answer queries as my schedule allows.
I would like to thank Ian Jamieson (U Otago), Catherine Grueber (now with San Diego Zoo Global), Murray Efford (U Otago), Jess Scrimgeour (NZ Dept. Conservation), and Michelle Reynolds (USGS) for helpful discussions that have greatly improved AlleleRetain. Funding for this work was generously provided by New Zealand Department of Conservation, Landcare Research, Marsden Fund, University of Otago, and Allan Wilson Centre for Molecular Ecology and Evolution.