We present a new method for establishing an alignment between a polyphonic musical score and a corresponding sampled audio performance. The method uses a graphical model containing both discrete variables, corresponding to score position, as well as a continuous latent tempo process. We use a simple data model based only on the pitch content of the audio signal. The data interpretation is defined to be the most likely configuration of the hidden variables, given the data, and we develop computational methodology for this task using a variant of dynamic programming involving parametrically represented continuous variables. Experiments are presented on a 55-minute hand-marked orchestral test set.