Hi there,
By default, the function returns conditional likelihoods: Pr (site | rate class). In your example, the probability of observing a site given the model in class 1 is 0.1, and given the model in class 2 is 0.3
Most of the time one wants Pr (rate class | site), which can be obtained by a simple application of the Bayes rule:
Code:Pr (rate class | site) = Pr (site|rate class) * Pr (rate class) / Pr (site)
Pr (site) is simply the sum of all Pr (site|rate class) * Pr (rate class) (the normalization factor), and Pr (rate class) can be obtained by calling
Code:ConstructCategoryMatrix (priors, lfID, WEIGHTS);
HTH,
Sergei
PS I could probably give you more pointers if I had a better idea of what the final objective was.