Dear Wayne,

They are probably just vanishingly small. STORE_ROOT_SUPPORT does not actually compute

Prob (root = X) (i.e summing over all possible internal nodes for a fixed root)

I should have stated that what it currently computes is more esoteric:

Prob (most likely ancestral nodes | root = X),

hence given a fixed root it computes the probability of the most likely assignment of ancestral state.

I can add the computation of Prob (root = X) as well if you want; it's being computed in the process anyway, just not output in any way.

Cheers,
Sergei