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Class Summary |
| Hmm |
The abstract class of Hidden Markov Models. |
| Hmm2 |
This is an abstract class for HMMs that are pair-HMMs and do not emit characters into
unobservable sequences. |
| HmmNonParam |
An implementation of the abstract pair-HMM that emits characters into non-observable sequences
Used when a new alignment is proposed that aligns together two substrings via an ancestral sequence. |
| HmmSilent |
This is the abstract class of pair-HMMs that emit characters into one unobservable
sequence, namely that aligns two observable sequences via an unobservable
ancestral sequence. |
| HmmTkf92 |
This class implements a simplified version of the TKF92 pair-HMM. |