I am trying to calculate molecular diversity indices for a SNP dataset in Arlequin (v 3.5), and I am having some issues. In the results file, I keep getting the message: 'unable to compute theta(hom) and theta(k) when all gene copies are different'. The program also seems to think that my sample size for each group is double what it actually is, despite the fact that I specified standard genotypic data and seem to have formatted my file for the correct ploidy. So unless the sample size refers to the number of haplotypes instead of the number of genotypes, something is wrong.
One of my coauthors sent me her .arp input file that she used to calculate theta(hom) and theta(k) for her SNP dataset so that I could double check that everything was formatted correctly in my file, and it is. I get the same message when I try to compute molecular diversity indices for her file, so it seems as though I must be messing up the settings somehow. The rest of the results file looks ok though. Any advice on what is going on here and how to troubleshoot would be very much appreciated... Many thanks!