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Over the last thirty years, the algorithms used for reconstructing ancestral gene orders from extant gene orders have evolved from methods that did not account for gene evolution (the Small Parsimony Problem) to methods relying heavily on the availability of reconciled gene trees. In this talk I will describe how ancestral gene orders reconstruction is a problem that can be related to both genome assembly and phylogenomics. I will use this point of view to review the evolution of ancestral gene orders reconstruction methods, and how the increasing use of gene trees has drastically changed the way the problem is addressed, especially toward handling uncertainty and ambiguity in proposed ancestral gene orders.