Pair hidden M arkov models
Marina Axelson-Fisk, Nicolas Bray, Lior S. Pachter · Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics · 2005
Abstract We describe pair hidden Markov models, with an emphasis on their relationship to evolutionary models and hidden Markov models. We then explain the statistical interpretation of alignment with pair hidden Markov models, and highlight connections to the Needleman–Wunsch algorithm and other dynamic programming–based alignment algorithms.