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並前往https://www.cs.rice.edu/~nakhleh/COMP571/Slides-Spring2015/SequenceAlignment-PairwiseHMM.pdf

Pairwise HMMs and Sequence Alignment

emitting an aligned pair a:b. States X and Y: emission probabilities q a for emitting symbol a against a gap. Emits a pairwise alignment instead of a single.

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