In the general setting of long-memory multivariate time series, the long-memory characteristics are defined by two components. The long-memory parameters describe the autocorrelation of each time series. And the long-run covariance measures the coupling between time series, with general phase parameters. It is of interest to estimate the long-memory, long-run covariance and general phase parameters of time series generated by this wide class of models although they are not necessarily Gaussian nor stationary. This estimation is thus not directly possible using real wavelets decomposition or Fourier analysis. Our purpose is to define an inference approach based on a representation using quasi-analytic wavelets. We first show that the covariance of the wavelet coefficients provides an adequate estimator of the covariance structure including the phase term. Consistent estimators based on a local Whittle approximation are then proposed. Simulations highlight a satisfactory behavior of the estimation on finite samples on linear time series and on multivariate fractional Brownian motions. An application on a real neuroscience dataset is presented, where long-memory and brain connectivity are inferred.