Using the Hidden Markov model for multilocus analysis requires to make two main assumptions.
Assumption G5. There is no crossover interference (NI), so that the inheritance vectors form a continuous time Markov chain along the length of the chromosomes.
Assumption G6. The markers are in linkage
equilibrium (LE).
We already encountered Assumption G5 in section 5.3. of week 3
in the context of experimental crosses. When the HMM is used in
linkage analysis Assumption G5 is usually stated, but there is
no mention of Assumption G6 which is a strong assumption.