The principal HMM algorithms are reviewed including alignment, training and model comparison.
Theory is developed for prediction of alignment accuracy and tested using simulations.
A model of evolutionary change in proteins - Dayhoff, Schwartz et al. Doc 30 A hidden Markov model that finds genes in E - Krogh, Mian et al. Jonassen et al. 1980 Doc 9 Improved splice site detection in Genie - Reese, Eeckman et al. Liu et al.