Figure 1.

Desired topology as cladograms. The figure shows six different trees, different permutations of the Neurospora topology that we attempted to recover from CGH data using a variety of methods. These trees are broken down into three groupings of taxa, CON (Figures 1A and 1B), NEU (Figures 1C and 1D), and ALL (Figures 1E and 1F). These are shown with and without the reference N. crassa A as some methods performed better without the reference taxon included. For this reason both versions of each taxon grouping were used to construct CGH phylogenies. Note that these cladograms do not reflect true branch length distances.