Influence of the number of loci on haplotype frequency estimation. A – Similarity index between the frequencies obtained by the used computer packages and the real haplotype frequencies. B – Comparison between the number of different haplotypes identified by the computer packages and the number of different haplotypes obtained by segregation study. C – Overall difference in haplotype frequencies between estimated and true values. The two-locus haplotypes were composed by Class II alleles (DQB1-DRB1), the three-locus haplotypes were composed by Class I alleles (A-B-Cw) and the five-locus haplotypes were the extended haplotypes (A-B-Cw-DQB1-DRB1), all with a sample size of n = 61 individuals. Unbroken line denotes comparisons of Arlequin V3.0 to real data; dotted line, comparisons between PHASE v2.1.1 and real data.