Birds and their flight have been a source of inspiration for humans for centuries. When flying in formation, they are able to save energy by exploiting the wakes of the individuals flying in front of them. Their wakes, however, are highly complex, unsteady and 3-dimensional and studying them cannot be done with simple models. In this presentation, we describe a model coupling biomechanics and fluid dynamics for the simulation of flapping flight, and its application to the study of bird wakes. Using an hybrid vortex particle-mesh method coupled with deforming lifting and dragging lines representing the birds, we compute and analyse the wake of birds flying in formation. We identify the main vortical structures of the wake and their evolution over large downstream distances, observing the shedding of a vortex sheet, its roll-up into separate vortices and the deformation and decay of these vortices as they are advected. We study the interactions between birds flying in formation. This shows the influence of the wake deformations on the potential energy savings. We finally compare the wake of a pair of flyers, compare it to that of a single bird, and draw conclusions regarding larger formations.