We address the problem of performing decision tasks and, in particular, classification and recognition in the space of dynamical models in order to compare time series of data. Motivated by the application of recognition of human motion in image sequences, we consider a class of models that include linear dynamics, both stable and marginally stable (periodic), both minimum and nonminimum phases, driven by non-Gaussian processes. This requires extending existing learning and system identification algorithms to handle periodic modes and nonminimum-phase behavior while taking into account higher order statistics of the data. Once a model is identified, we define a kernel-based cord distance between models, which includes their dynamics, their initial conditions, and input distribution. This is made possible by a novel kernel defined between two arbitrary (non-Gaussian) distributions, which is computed by efficiently solving an optimal transport problem. We validate our choice of models, inference algorithm, and distance on the tasks of human motion synthesis (sample paths of the learned models) and recognition (nearest-neighbor classification in the computed distance). However, our work can be applied more broadly where one needs to compare historical data while taking into account periodic trends, nonminimum-phase behavior, and non-Gaussian input distributions.