What are hidden Markov models, ... multiple sequence alignment and ... because they assume that each residue depends only on one underlying state. An example where HMMs are usually inappropriate ...

C. Bracken, B. Rajagopalan, & E. Zagona (2014). “A Hidden Markov Model Combined with Climate Indices for Multi-decadal Streamflow Simulation,” Water Resources Research, 50, 7836-7846. Abstract: ...