Figure 3
From: Evolutionary models for insertions and deletions in a probabilistic modeling framework
A pair-HMM model. Description of a pair-HMM model. The three states: Emit-a-pair (XY), Emit-X (X), and Emit-Y (Y) have four possible transitions each, which we are going to make time-dependent functions. This a geometric model, in which the expected length is given by 1/Ï„. In order to generate alignments with the same expected length at all times, we will leave the parameter Ï„ (the transition of each of the three states into the exit state) unchanged with time. The figure shows the transition probabilities having the following properties: 
, 
, 
, 
. These properties guarantee that the model is reversible.