Figure 5

Example showing constraints of triallelic SNP site. Assume a triallelic SNP site and an individual with the allele composition (0, 1, 2, 2). First, the alleles are encoded to their corresponding binary representation, here 0 ≡ 00, 1 ≡ 01 and 2 ≡ 10. Second, each allele is recoded to binary variables $v_{i,j}^{l,1}$, $v_{i,j}^{l,2}$ and $v_{i,j}^{l,3}$, with 1 ≤ l ≤ 4. Finally, the three vectors are constrained to the corresponding sum.