Fig. 4
From: Parameterizing sequence alignment with an explicit evolutionary model
A symmetric evolutionary pair HMM. State machine representation of the AFR evolutionary model in joint form, where the X/Y state symmetry (reversibility) is obvious. The AFR model is a fragment derivative of the Linear Reversible (LR) model. We use capital letters for the transition probabilities in order to remember that these are joint probabilities. The normalization of the model may not be apparent from this representation. One should remember the reversibility condition of the LR model, given by \(\beta _{t}^{\textsc {lr}} = p^{\textsc {lr}}(1-\beta _{t}^{\textsc {lr}})\gamma _{t}^{\textsc {lr}}\)