Estimation of the true evolutionary distance under the fragile breakage model

Motivation: The ability to estimate evolutionary distance between extant genomes plays a crucial role in many phylogenomic studies. Such distance is often measured as the number of genome rearrangements (such as reversals, translocations, fusions, and fissions) between genomes. This measure is traditionally based on the parsimony assumption, implying that the evolutionary distance between two genomes can be approximated as the rearrangement distance equal the minimal number of genome rearrangements required to transform one genome into the other. However, in reality the parsimony assumption may not always hold, emphasizing the need for estimation that does not rely on the (minimal) rearrangement distance. The evolutionary distance that accounts for the actual (rather than the minimal) number of genome rearrangements between two genomes is often referred to as the true evolutionary distance.