Reconstructing ancestral gene orders in the presence of duplications is important for a better understanding of genome evolution. Current methods for ancestral reconstruction are limited by either computational constraints or the availability of reliable gene trees, and often ignore duplications altogether. Recently, methods that consider duplications in ancestral reconstructions have been developed, but the quality of reconstruction, counted as the number of contiguous ancestral regions found, decreases rapidly with the number of duplicated genes, complicating the application of such approaches to mammalian genomes. However, such high fragmentation is not encountered when reconstructing mammalian genomes at the synteny-block level, although the relative positions of genes in such reconstruction cannot be recovered.