We propose a frequency domain adaptive algorithm for wave separation in wind instruments. Forward and backward travelling waves are obtained from the signals acquired by two microphones placed along the tube, while the separation filter is adapted from the information given by a third microphone. Working in the frequency domain has a series of advantages, among which are the ease of design of the propagation filter and its differentiation with respect to its parameters. Although the adaptive algorithm was developed as a first step for the estimation of playing parameters in wind instruments it can also be used, without any modifications, for other applications such as in-air direction of arrival (DOA) estimation. Preliminary results on these applications will also be presented.