FIG. 4.

Heat map showing the percentage of sequences, among those assigned to each node (columns), that match each of the patterns (rows) associated with the root node contrast alignment for the de novo PRTaseII hierarchy. Plotted above the map are the values of subLLR(z,h) for the zth node and where h corresponds to the root; node identifiers are listed in the row directly below the map. Node identifiers are highlighted using the subtree color scheme given in Figure 3. Note that all of the nodes in two of the subtrees (highlighted in purple and orange) contribute negatively to the LLR. Nodes are ordered by decreasing percentages of overall matches to the patterns; note that this fails to correspond to decreasing values of subLLR(z,h) because the number of sequences (shown in the bottom row) influences this value, but not the percentage of matches. The contributions (in nats) of patterns, denoted by subLLR(j,h), are given in the far right column.