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. 2009 Sep;10(6):402–415. doi: 10.2174/138920209789177575

Fig. (3).

Fig. (3)

Example of a pair hidden Markov model. A pair-HMM generates an aligned pair of sequences. In this example, two DNA sequences x and z are simultaneously generated by the pair-HMM, where the underlying state sequence is y. Note that the state sequence y uniquely determines the pairwise alignment between x and z .