Table 2.

Algorithm to sample an IBD graph on n individuals from SNP data

1	Initialize ${\mathbf{p}}_{2n}^{\mathit{pop}}$ to the empty IBD graph.
2	Randomly permute the individuals and label them {A1 … An}
3	Sample from Q[p4(A1A2)|x(A1A2)] and add the trajectory to ${\mathbf{p}}_{2n}^{\mathit{pop}}$.
4	For 2 < k ≤ n
5	Randomly permute individuals {A1 … Ak−1} and label them {B1 … Bk−1}.
6	For 1 ≤ i < k
7	Sample from $Q[{\mathbf{p}}_4(B_i{A}_k)\mid {\mathbf{p}}_{2n}^{\mathit{pop}},\mathbf{x}(B_i{A}_k)]$, x(BiAk)] and add the trajectory to ${\mathbf{p}}_{2n}^{\mathit{pop}}$.
8	End for I
9	End for k
10	Return an IBD graph on n individuals, ${\mathbf{p}}_{2n}^{\mathit{pop}}$.