Figure 4
From: More accurate recombination prediction in HIV-1 using a robust decoding algorithm for HMMs
Computing the probability of a footprint. To compute the probability of a footprint f = f1, . . . , f k , we create a group states G i for each entry in f, corresponding to the states in M labelled f i . A path compatible with the footprint must first go from x0 to one of the states in G1, then eventually go to G2, and on to G k . Transitions are only allowed from G i to G i or Gi+1.