Scaffold Generated in the Presence of Safe Inversions. Illustration of the example discussed in the text of a genome with 40 conserved blocks with respect to a reference genome. The query genome and the reference genome differ by seven safe inversions, denoted by the nested horizontal square brackets. The conserved blocks appear in nine contigs. The permutation on the top is the “real” query genome, and the permutation at the bottom is the scaffold reconstructed by the algorithm. The bars with alternating colors help visualize inversion signatures.