First we should notice that our model of evolution treats each
position independently of its neighbours.
Hence the probability of an EC will be the
product of the probabilities for each of the aligned positions.
For each aligned position we have an EPT with one amino acid at
(We consider the special case of indels later).
The tree in Figure 2 represents a slice
of the EC at position 4
where sequence 1 has a K, sequence 2 has an R, etc.
In this case, the amino acids placed at nodes W, X and Y are the
unknown amino acids at the divergence points.