Interleaved HMM. The interleaved HMM with coupled hidden chains used in the OVERPAINT model to compute [adapted from Figure two(b) of ]. h k+1,j is the allele state at the j th site of haplotype h k+1. X
denote the j th hidden state of the crossover and gene conversion chain, respectively, and their joint configuration determines the index of the haplotype from which h k+1,j is copied.