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We propose a general method of constructing Wannier functions in disordered systems directly out of energy eigenstates. This method consists of two successive operations: (i) a phase transformation setting the proper localization center; (ii) the mixing of adjacent states in energy to sufficiently minimize the spread of the Wannier functions. The latter operation can be well approximated by a band matrix, further facilitating the calculation. Detailed implementation of our method is illustrated with one dimensional systems; the generalization to higher dimensions is straightforward.

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