I have data from nine microsatellite loci and MHC class II gene data where I cannot assign alleles to loci (however I know that I have multiple loci in individuals because I can amplify up to 8 MHC alleles with my primers). I want to compare FST values of fish from different populations using both markers. To do so (following the literature), I have to calculate FST values using binary-encoded data with each allele considered as separate dominant locus (present 1 / absent 0). Again following the literature, calculating FST values based on these binary data should be possible using ARLEQUIN. However I have problems with my input file. I have used ARLEQUIN quite often to calculate pairwise FST values or do ANOVAS with "normal" microsatellte data or allele frequencies but I just do not know how an input file with binary data for microsatellites (or MHC) should look like??? Or is there a program that can be used to convert to binary data?

Does anybody have experience with this kind of analysis and can help me or would be willing to share an input file for ARLEQUIN so that I have an idea how this should look like?

Looking forward to your answers