Assume that we are given two trained HMM models of diploidgenotypes
(i.e. two haplotypes per individual) for two di erent populations,such
that each HMM models the same haplotypes of length m (i.e. mSNPs)
with k states at each SNP (i.e. a total of 2k states across the twomodels).
The transition probabilities now also describe the probability ofmoving
between each pair of states coming from the two di erentmodels.
We wish to de ne a test for the local ancestry of a particularsegment
in the genome. Speci cally, let W be a segment of interest oflength w
(i.e. a substring of the haplotype), given an input genotype g, wewant
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