Résumé
The reconstruction of the chromosomal organization of ancient genomes has many applications in comparative and evolutionary genomics. Here we propose a novel, methodological, use for these predicted ancestral syntenies, directly focused on phylogenomics. It is a way to assess the accuracy of gene trees and species trees. We use a method that reconstructs, from gene trees and extant gene orders, ancestral adjacencies, i.e. the immediate neighborhood between pairs of genes, independently for each pair. This independence allows to split the computations into many independent problems that can each be solved exactly using efficient algorithms, but might result in sets of ancestral adjacencies that are incompatible with the expected linear or circular structure of chromosomes. We show here that this drawback can actually be turned into a useful 1 This work benefited from the support of ComputeCanada.