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We discuss how to construct tight-binding models for ultra cold atoms in honeycomb potentials, by means of the maximally localized Wannier functions (MLWFs) for composite bands introduced by Marzari and Vanderbilt [1]. In particular, we work out the model with up to third-nearest neighbors, and provide explicit calculations of the MLWFs and of the tunneling coefficients for the graphene-lyke potential with two degenerate minima per unit cell. Finally, we discuss the degree of accuracy in reproducing the exact Bloch spectrum of different tight-binding approximations, in a range of typical experimental parameters.

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