I am trying to understand the connection between viterbi, NW and Baum Welch.
From my understanding, NW is the Viterbi algorithm applied to a pair HMM.
So given two sequences, you will obtain the optimal alignment.
Now my question is whether there is something analogous to the Baum-Welch algorithm for the pair HMM.
If there exists one, what is it called and what does it output?
If Viterbi for pair HMMs outputs the optimal alignment given two sequences then will the BW equivalent optimize the pair HMM parameters given the 2 sequences?