Figure 5.
Building the BEAGLE HMM
(A) Building level l+1 from level l. The first step is merging. In this example, states S1, S2, and S4 are merged, and states S3 and S5 are merged. After merging, haplotype clusters are split on the basis of the allele at marker l+1. All haplotypes in states S7 and S10 have allele 1 at this marker, whereas all haplotypes in states S8, S9, and S11 have allele 2.
(B) Transition probabilities between the states at the two levels. All transitions with nonzero probabilities are shown. Transitions with the same probability have the same pattern on the arrow shaft.