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In multi-Higgs-doublet models the alignment in flavour space of the relevant Yukawa matrices guarantees the absence of tree-level flavour-changing couplings of the neutral scalar fields. We analyze the consequences of this condition within the two-Higgs-doublet model and show that it leads to a generic Yukawa structure which contains as particular cases all known specific implementations of the model based on Z_2 symmetries. All possible freedom in the Yukawa sector gets parametrized in terms of three complex couplings. In spite of having flavour conservation in the neutral scalar couplings, the phases of these three parameters represent potential new sources of CP violation.

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