AlleleRetain is described in:
Weiser, E. L., C. E. Grueber, and I. G. Jamieson. 2012. AlleleRetain: A program to assess management options for conserving allelic diversity in small, isolated populations. Molecular Ecology Resources 12:1161-1167.
AlleleRetain is also used in:
Detailed guidance provided by the New Zealand Department of Conservation for establishing reintroduced populations of native birds.
Grueber, C.E., Fox, S., McLennan, E.A., Gooley, R.M, Pemberton, D., Hogg, C.J., & Belov, K. 2018. Complex problems need detailed solutions: Harnessing multiple data types to inform genetic management in the wild. Evolutionary Applications: Accepted Article.
Buckland, S., Cole, N.C., Groombridge, J.J., Küpper, C., Burke, T., Dawson, D.A., ... & Harris, S. 2014. High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation. PloS One 9:e93387.
Liu, G., Shafer, A., Zimmermann, W., Hu, D., Wang, W., Chu, H., ... & Zhao, C. 2014. Evaluating the reintroduction project of Przewalski’s horse in China using genetic and pedigree data. Biological Conservation 171:288-298.
Reynolds, M. H., Weiser, E., Jamieson, I., & Hatfield, J. S. 2013. Demographic variation, reintroduction, and persistence of an island duck (Anas laysanensis). Journal of Wildlife Management 77:1094-1103.
Weiser, E.L., C.E. Grueber, and I.G. Jamieson. 2013. Simulating retention of rare alleles in small populations to assess management options for species with different life histories. Conservation Biology 27:335-344.
Please let me know if your paper is not included in the above list!