the E-step of EM, and the totals are used in the M-step. This is equivalent to specifying a Dirichlet prior for probability parameters, or a gamma prior for rate parameters. An example, for HKY85: (pseudocounts (piA 36.0195) (piC 29.0076) (piG 37.0184) (piT 35.0149) (alpha 1.01919 1.67501) (beta 2.03806 3.3364)) Markov chains