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We consider the running of the neutrino mass matrix in the Standard Model and the Minimal Supersymmetric Standard Model, extended by heavy singlet Majorana neutrinos. Unlike previous studies, we do not assume that all of the heavy mass eigenvalues are degenerate. This leads to various effective theories when the heavy degrees of freedom are integrated out successively. We calculate the Renormalization Group Equations that govern the evolution of the neutrino mass matrix in these effective theories. We show that an appropriate treatment of the singlet mass scales can yield a substantially different result compared to integrating out the singlets at a common intermediate scale.

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