Table 8.

Proteobacteria Tree Accuracy Analysis. The scaled Robinson-Foulds (RF) distances [40] of the trees produced from the Proteobacteria dataset using fixing a model used to build trees from each alignment. The values reported are the median and average distance computed by comparing every tree against every other tree. When the optimal set of models were used the median was 0.22 and the average was 0.34. Phyml [53] was used to build all trees.

Model	Median RF	Mean RF	Model	Median RF	Mean RF
Blosum	0.23	0.35	JTT	0.23	0.34
Blosum+I	0.25	0.35	JTT+I	0.25	0.35
Blosum+G	0.25	0.35	JTT+G	0.25	0.35
Blosum+I+G	0.25	0.35	JTT+I+G	0.25	0.35
CPREV	0.24	0.35	MtREV	0.25	0.35
CPREV+I	0.25	0.35	MtREV+I	0.25	0.35
CPREV+G	0.25	0.35	MtREV+G	0.25	0.35
CPREV+I+G	0.25	0.35	MtREV+I+G	0.25	0.35
Dayhoff	0.2	0.34	WAG	0.21	0.34
Dayhoff+I	0.21	0.34	WAG+I	0.23	0.35
Dayhoff+G	0.22	0.34	WAG+G	0.25	0.35
Dayhoff+I+G	0.22	0.34	WAG+I+G	0.25	0.35