Methods. A) Graph compression to eliminate accessory genes in backbone stability calculation; B) Two hypothetical genome comparisons to illustrate the effect of rearrangements on the diameter of the graph. The chromosomes under comparison have 600 genes each (two clusters of genes are compressed into rectangular nodes). In the comparisons, the two chromosomes differ in the position of gene 1, they have the same number of genes, and therefore the same diameter (D). Let us focus on the networks obtained after combining the chromosomes under analysis: as a consequence of the different positions of gene 1 in the two chromosomes under comparison, new edges are formed between them, and this affects the diameter of the combined graph. When rearrangements involve distant loci (left), there is a strong effect on the diameter (in the example, it halves). On the converse, rearrangements between nearby loci (right) have a weak effect on the diameter.