Figure 1

1a displays a PCA of the variation between the distance matrices. Each point is named after either the phylogenetic method used to create the matrix or in the case of CR the conditioning genome used. The size of the points is proportional to the size of the conditioning genome used. Figure 1b depicts PCA analysis of the 100 bootstrap replicates from each of the gene-content methods and the 22 variants of CR using one genome. Finally 1c displays a matrix produced using Methanosarcina acetivorans as the conditioning genome. The columns representing Methanococcus jannaschii and Methanosarcina mazei in the distance matrixhave been plotted. The dots on the plot represent the distance between the labeled genome and Mco. jannaschii (plotted on the x axis) and Methanosarcina mazei (plotted on the y-axis).