Label the original haplotypes as X1, X2, ..., XH and the distinct unique haplotypes as Y1, Y2, ..., YU. For example, in Figure 1, block B bounded by markers P = 1 and Q = 6 has U = 3 distinct haplotypes. Let Lk(.) and Lk(.) denote the left probabilities for the original states and reduced states at marker k (ref. 29). Assuming we know LP(X1), ..., LP(XH), equation (1) allows us to obtain Lp(Yi) for each distinct haplotype. (1)LP(Yi)=∑j=1,…,HandXj=YiLP(Xj)
