Since different populations or breeds have different genetic background, the allele frequency or genotype frequency of different populations may differ from each other significantly. HIBLUP can integrate the population classification information into several genomic analysis, e.g., allele or genotype frequency calculation, genomic relationship matrix construction, single or multiple traits model fitting. The population classification file is easy to prepare, two columns are required, the first is the list of individuals names and the second is the detailed classification of each individual. For example:
ID Breed Ind1 DD Ind2 YY Ind3 LL Ind4 YY Ind5 LL
The file should be assigned to parametric option --pop-class.