Figure 6.

Simplified representation of the GTR model of Figure 5b using a tree plate. The tree plate, a big dashed box, divides the nodes into three classes: the root node, internal nodes and tip nodes. The character state variables are named S_ij where i denotes the i-th node and j the j-th site. The root node does not have a parent node in the tree while the other nodes do. The internal nodes and the tip nodes depend on the ancestral states. The ancestral variable of node i is obtained using the parent indicator function $\tilde{p}(i)$. Tip nodes are clamped and thus shaded. A tree topology is attached to the tree plate via the tree variable Ψ shown on the left. The tree variable informs the plate of the structure and if the tree variable changes, the structure of the resulting graph changes too.