I've heard of Markov Chains, but I didn't understand them until I visited this site that explains them with simple interactive animations. Look at the illustration above.

Statistical models called hidden Markov models are a recurring theme in computational biology. What are hidden Markov models, and why are they so useful for so many different problems?

Welton et al (2005) describes how these partially observed data can be used to inform a Markov rate matrix, and takes a Bayesian statistical approach using the WinBUGS software. The paper covers: ...