Thank you for all the answers. There is a listing of all the answers I received. Unfortunately, it seems that no software is able to compute automatically C.I. of pairwise FST. I checked all the softwares that are mentioned in those answers and I can confirm that no one fulfilling my requirements. I decided to use the solution (the hard and long one...) proposed in the first answer included in this message. With a good work technique it takes me about 4 hours (instead of 1-2 day) to calculated CI for 277 pairwise comparisons. Good luck and many thanks again! Philippe. Original message: Does somebody know a software allowing the estimation of confidence intervals for pair-wise Fst using bootstraps over loci? It seems that both Arlequin 3.01 and Fstat are only able to estimate confidence intervals for the overall Fst. Thank you. ===I asked the same question about 8 months ago and received a lot of software suggestions, including GENEPOP, MSA, SPAGEDI, POPDIST, GENETIX and the ones you've already mentioned. However, browsing through the software I did not find any of them fulfilling my requirements (Newer versions might include what you are looking for). After spending weeks trying out and searching for appropriate software, I found that creating FSTAT inputfiles for each pair of populations and obtaining 95% CI for the overall Fst was the best (only?) solution. Know its a very tedious way around the problem, but with <100 pairs, good copy/paste skills and music on the ipod it should be possible to do in a day or two... ===I encountered the same problem in a study of ours. I decided to use "Resampling Stats" to calculate a bootstrapped "average pairwise Fst) across all our AFLP-loci. Maybe this is not the most elegant way how to do it, but it is at least one way to do it! ===I'm not aware of any software that can perform that task. I've recently had the same problem and ended up analysing 66 datapools seperately (in FSTAT) to get the C.I's on pairwise Fst's. Just a couple a weeks ago there was quite a similar question here on Evoldir concerning C.I.'s on Fis values on subpopulation-level. It seems to me that there is a big need for a piece of software to calculate C.I's on all levels. RSTCALC will calculate all the desired C.I's and tests, but only on Rst values. Guess that wasn't much help, but if you get some usefull replies, please post the answers. ===I believe TFPGA (free software) will accomplish what you're looking for. Here is the URL: http://www.marksgeneticsoftware.net/tfpga.htm TFPGA provides "Theta-P" values, but these are equivalent to Fst. ===You can do this in GDA (Genetic Data Analysis - Paul Lewis - free download from Paul's Web site). You'll have to select on pair of populations at the time, although (easily done within the program, ie you don't have to change the input file). Have you considered using permutation to test for the significance of your pairwise Fst values? This can be easily done in Fstat or Genetix. ===I have used GDA (http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php) for some of these types of calculations. In a single dataset with multiple populations, you can 'Exclude' (using the 'Misc.' menu) all populations but two, then calculate an FST and bootstrap over loci (options within the F-stats menu) to get a confidence interval. In order to change parameters of the bootstrap, go to F-stats --> Options --> Options for bootstrap. Unfortunately, you would have to do this for each pair of populations, but it seems to work well. Good luck! ===The program GDA (Genetic Data Analysis; Lewis and Zaykin 1999) will bootstrap over loci to give confidence intervals for pairwise Fst (theta). You have a be a little tricky to get the estimate though. Once you input your data into GDA, it will give you the option of excluding populations from each analysis. You have to exclude all populations but the two that for which you are interested in getting a pairwise estimate, and then estimate Fst and bootstrap over loci for the confidence interval. It won't give confidence intervals for the estimates in the pairwise theta matrix it estimates. It takes a bit longer this way, but I don't know of other programs that will give confidence intervals for pairwise estimates. GDA can be found at : http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php philippe.girard@umontreal.ca