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  HyPhy Documentation: Miscellaneous: Spatial Rate Correlation via HMMs

      HYPHY implements the method of Felsenstein and Churchill (1996) ( as described in "A Hidden Markov Model Approach to Variation Among Sites in Rate of Evolution". Mol. Biol. Evol. 13(1) :93-104), with the extension that the rates are not fixed a-priori, but rather sampled from one of the predefined distributions, and the auto-correlation parameter lambda is estimated.

The Hidden Markov chain model assumes all rates to be equiprobable and the uses the transition matrix with entries as follows:

where N is the number of rate categories, and lambda is in [0,1]. If we define

then L+1 is the expected length of a patch of sites with the same rate.

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002