Backbone and genome organization stability. The scheme shows how we encode and combine individual chromosomes for their comparison; nodes (A to G) represent genes; edges between nodes indicate that the genes are contiguous on the chromosome. The figure provides examples illustrating the difference between backbone and genome organization stability. Since we deal with pairwise comparisons, we are not able to differentiate deletions from insertions. Thick edges correspond to conserved gene neighborhoods (present in both genomes). The two stability measures are identical when there are no accessory genes (first two colums).