I had the same problem. In fact, I had to use free genetic software, Arlequin for this purpose.
If you already have each genotype assigned to any cluster, then use AMOVA technique (genetic version of ANOVA) in order to find out if there are significant differences between clusters or if some are overlapping.
Moreover, Arlequin also computes differences between populations (clusters) using many indices.
If you also want to use any genetic software for clustering, then I recommend to use another free genetic software, Structure.
Genetic data should be analyzed with genetic software or special genetic packages since they often need special measures of similarity of special methods of analysis (AMOVA, model-based clustering in Structure software).