Balanced Topology Results. Figure 3A is a cladogram of an eight taxa balanced tree topology. In our simulation a sequence alignment was created using this input tree as a guide, where the branch lengths govern the number and pattern of substitutions. A number randomly drawn from a Gaussian distribution, empirically determined from published yeast genomic data, was used to multiply these branch lengths to produce a set of genes evolved for a range of substitution rates. The average of each range of substitution rates is indicated under each column. Figure 3B shows the symmetric distances for 200 simulation runs of the correlation-based NJ analysis evolved at the average sequence divergence indicated. Columns 1-3 use taxon A as the reference, Columns 4-6 use taxon H. Zero steps indicate perfect agreement between the input topology and the trees output by the simulation (red portions). One step away indicates a single collapsed branch (orange portions). A mispairing of two taxa is given a score of two (yellow portions). Scores in subsequent figures are cumulative and color-coded as indicated in the chart legends. Figure 3C shows the stacked histogram for the symmetric distances from the input topology for 100 replicate NJ trees calculated with the Euclidean distance metric. The order for reference taxa is the same as above. The stacked histogram in Figure 3D is of the symmetric distances from the input tree for 100 replicate 50% Majority-Rule Parsimony (PMR) trees. An example of this topology, two steps away from the reference, is given in Figure 4B.