Hidden Markov Model

http://a-little-book-of-r-for-bioinformatics.readthedocs.org/en/latest/src/chapter10.html

https://www.quora.com/What-is-a-simple-explanation-of-the-Hidden-Markov-Model-algorithm/answer/Deepthi-Sen?srid=dNzz&share=1

http://www.nature.com/nbt/journal/v22/n10/abs/nbt1004-1315.html

An Introduction to Hidden Markov Models for Biological Sequences - http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.85.7972&rep=rep1&type=pdf

http://stats.stackexchange.com/questions/47846/how-to-define-initial-probabilities-for-hmm

http://homepages.ulb.ac.be/~dgonze/TEACHING/viterbi.pdf