Gene order alignment on trees with multiOrthoAlign

We relate the comparison of gene orders to an alignment problem. Our evolutionary model accounts for both rearrangement and content-modifying events. We present a heuristic based on dynamic programming for the inference of the median of three genomes and apply it in a phylogenetic framework. multiOrthoAlign is shown accurate on simulated and real datasets, and shown to significantly improve the running-time of DupLoCut, an "almost" exact algorithm based on linear programming, developed recently for the same problem.