Pair HMM is widely used in DNA alignment.
For each HMM, there are 3 sets of characteristic parameters:
1) transitional probabilities
2) emission probabilities
3) initial probabilities
I understand how to use how to solve the alignment problem once we have a HMM.
But I don't know how we get the parameters of a HMM in the first place.
Can anyone give me an answer or references to related material?