I am using lositan to try and pick out outliers from a couple of large SNP datasets. I have three input files both in genepop format, two of these contain only two populations and one contains 5. When I load one of the two population files into lositan it has no problems, the file will load and run fine but when I load in the other it gets as far as loading population 2 and freezes. The program doesn't freeze completely, I can still look at menu options and the number of loci and populations it shows in the total data are correct but nothing happens (for days), it doesn't give me an Fst value and I can't run the simulation.
When I load the third file in (the one with 5 populations), if I try to use all of the populaitons it works fine but when I try to use only two of the 5 populations (in the data used menu option) I get the same problem, it says loading population 2 but never gets any further.
As one of the files runs with no problems and the other two are identical in format I don't think it can be the input file but have no idea what could be the problem. As the lositan site says to ask for help on here I was hoping someone might be able to tell me what is going wrong?