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It is shown how to reconstruct the stacking sequence from the pairwise correlation functions between layers in close-packed structures. First, of theoretical interest, the analytical formulation and solution of the problem are presented when the exact pairwise correlation counts are known. In the second part, the practical problem is approached. A simulated annealing procedure is developed to solve the problem using as initial guess approximate solutions from previous treatments. The robustness of the procedure is tested with synthetic data, followed by an experimental example. The developed approach performs robustly over different synthetic and experimental data, comparing favorably with the reported methods.