Principal component analysis on mutation spectrum, both with and without partitioning the genome. Each point represents a different clade. Note that although the points for the partitioned clades are differently positioned, the shift is consistent across clades indicating that the differences between clades are not driven by just one genome partition. The chart is interactive:

• mouse over points for details
• click on specific clades in the legend to highlight their points
• clck on the “exclude top” legend to show only points +/- exclusions of top mutations.
• shift-click to make multiple selections

Note that the PCA itself is not re-calculated even when some points are de-selected for display.