PAM (Dayhoff) matrices
The point accepted mutation (PAM) substitution model, also known as the Dayhoff substitution model, is an amino acid substitution model derived from empirica...
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COMP571 (Fall 2022)
Important note: The information contained in the course syllabus, other than the absence policies, may be subject to change with reasonable advance notice, a...
Backward algorithm
Like the forward algorithm, we can use the backward algorithm to calculate the marginal likelihood of a hidden Markov model (HMM). Also like the forward algo...
Forward algorithm
The Viterbi algorithm identifies a single path of hidden Markov model (HMM) states. This is the path which maximizes the joint probability of the observed da...
Viterbi algorithm
The Viterbi algorithm is used to efficiently infer the most probable “path” of the unobserved random variable in an HMM. In the CpG islands case, this is the...