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The calculation of orbital fluctuations and of the phase-orbital correlation within Floquet-based noise analysis of autonomous systems requires the availability of all the direct and adjoint Floquet eigenvectors associated with the noiseless limit cycle. Here the authors introduce a novel numerical technique for their frequency domain determination. The algorithm is entirely based on the Jacobian matrices already available from the harmonic balance-based calculation of the limit cycle, thus avoiding any time-domain integration. The Floquet eigenvalues and adjoint eigenvectors are calculated from a generalised eigenvalue problem, thus making the approach readily implementable into CAD tools provided that the Jacobian matrices are made available.