A rooted phylogenetic tree of Bacteria computed from representative proteins. As explained in the text, this tree was computed first altogether, then with an outgroup of Aeropyrum and Methanopyrus to place the root, and then again in overlapping halves using different proteins, with the split at the doubled edge near Chlorobium. The numbers indicate bootstrap support for clades out of 100 trials; omitted numbers are all 100. The bootstrap support for the root is 44; the second choice is shown dashed. The weakest bootstrap support is for the Spirochaetes and Chlamydiales clade; again the second choice is shown dashed. The Chloroflexus genome is available only in a draft; we give it a tentative placement, without bootstrap support or edge lengths, based on about 1200 columns.