Simulations were also used for a quantitative assessment of SeqTrack's performances. Data sets were obtained Reconstructing disease outbreaks T Jombart et al by simulating genealogies of haplotypes evolving stochastically in time and space. A detailed description of these simulations, along with scripts allowing to reproduce them, are provided in Supplementary Information. Two types of simulations, differing in the process governing the spatial spread of the isolates, were performed. The first scheme allowed isolates to disperse on a 5 Â 5 spatial grid according to a random Poisson process, with identical probabilities to move in all directions (Supplementary Figure S1 ). This scheme is later referred to as 'homogeneous diffusion'. The second type of simulations used stochastic dispersal based on predefined connectivity between locations, in which we specified the probabilities of migration between every pair of locations. This allowed us to recreate a spatial dynamic of 'sources' and 'sinks' with some locations seeding many other locations, including distant ones, and other locations attracting migration but hardly seeding other places (Supplementary Figure S2) . This type of simulation is later referred to as 'heterogeneous dispersal'. For each simulation scheme (homogeneous and heterogeneous dispersal), 10 genealogies of isolates simulated over 20 generations were obtained. Ten random samples of 800 isolates were then drawn from the genealogies, yielding 200 data sets that were analyzed. Simulations and analyses were performed on the computer cluster of the Centre de Calcul de l'Institut National de Physique Nucléaire et de Physique des Particules (CCIN2P3; http://cc.in2p3.fr/).