Thank you to all of you who replied. I have now edited the replies to my question of calculating Fis using user selected allele frequencies. Here are the answers: 1. I'm not sure if the program fits your needs perfectly, but I've recently found the program COANCESTRY (Wang 2010, accessible at http://www.zsl.org/science/research/software/coancestry,1360,AR.html very useful. You can use it to look at various measures of relatedness and F from both imported genetic data and by use of simulation. Hope this helps, Sarah Roels Ecology and Evolutionary Biology University of Kansas 2. I think that you can use the GENETIX permutation test. This test produces the sampling distribution of Fis based on your actual sample, but you can then use your "user Fis" and see where it is in this distribution. However, your approach is quite a mystery for me: how can you test desviation of a parental Fis value in a progeny sample He? These are actually 2 populations, so just because of genetic drift from one generation to the other you may have a different Fis than expected in your sample progeny. Sylvain Sylvain FAUGERON Assistant Professor Departamento de Ecologia Facultad de Ciencias Biologicas P. Universidad Catolica de Chile Alameda 340 Santiago CHILE Phone: (56) 23 54 26 47 Fax: (56) 23 54 26 21 e-mail: sfaugeron@bio.puc.cl 3. You could set up an excel spreadsheet to calculate the expected genotype frequencies using the previous generation. Kevin Roe Natural Resource Ecology and Management 339 Science II Iowa State University Ames, IA 50011 515 294-8332 kjroe@iastate.edu Africa Africa Gomez Advanced NERC Research Fellow Department of Biological Sciences University of Hull Cottingham Rd. Hull, HU6 7RX U.K. Tel: +44 (0)1482 465542 Fax: +44 (0)1482 465458 e-mail: a.gomez@hull.ac.uk http://www2.hull.ac.uk/science/biological_sciences/people/academic_staff/africa_gomez.aspxl Africa Gomez