Updating equations for the prior site type probabilities
We first derive the updating equations for the prior site type probabilities![$ f_s, s \in S$](img115.gif)
![$ t$](img131.gif)
![$ n_1,...,n_k$](img144.gif)
Now, for we use our current value for
, and if we further insert the expression for
(27.2) we get:
We get the updating equation for the prior site type probabilities,
, from equation 27.5: Let
index the sites in the alignment (
). Given the current values for the set of site frequencies,
, and the current values for the set of error probabilities, we obtain updated values for the site frequencies,
, by summing the site type probabilities given the data (as given by equation 27.5) across all sites in the alignment: