Does anybody know of a program which can calculate p values for pairwise Fis (inbreeding coefficient) comparisons? Most standard freeware programs I know give you an Fis for individual populations but don't come up with a pairwise Fis comparison between populations, i.e. is Fis of population 1 significantly different from Fis of population 2. If the software comes up with a standard error for Fis for each population you can work it out yourself but it would be great if that was done automatically for each population comparison.
Thanks for your help!
What about Fstat? But be warned - see this discussion: http://network.nature.com/groups/popgen/forum/topics/8802
Hi Aaron,
Unfortunately Fstat doesn't do it. Regarding the warning and the link this is about Fst - and I agree it's pretty futile to put p values on Fst as natural populations will be different unless there's clonal reproduction. However, it's different for Fis and I think it's valuable to find out whether there's a significantly higher level of inbreeding in one population compared to another one (example: adult - seedling comparison).
Yes, but the difference is only a matter of scale (they are essentially calculated the same way). But I see your point - what is your data?
Genepop (http://kimura.univ-montp2.fr/~rousset/Genepop.htm) will do this too.
Peter H. - are you sure Genepop can also do this? Tried to run diveRsity but get nothing but error messages when following the tutorial...
Me again... after failing with diveRsity and not finding it on Genepop, I went back to FSTAT, which seems to estimate 95% and 99% CIs (rather than p-values) after all (Fis is called Smallf for some reason):
http://genome-lab.ucdavis.edu/Links/ECL%20290%20Winter%202007/week%205/fixed_handout_for_290_2-2-07_FSTAT[1].pdf