The new PHOENIX code is discussed together with a sample of many new results that are obtained concerning magnetohydrodynamic (MHD) spectra of axisymmetric plasmas where flow and gravity are consistently taken into account. PHOENIX, developed from the CASTOR code [W. Kerner, J.P. Goedbloed, G.T.A. Huysmans, S. Poedts, E. Schwarz, J. Comput. Phys. 142 (1998) 271], incorporates purely toroidal, or both toroidal and poloidal flow and external gravitational fields to compute the entire ideal or resistive MHD spectrum for general tokamak or accretion disk configurations. These equilibria are computed by means of FINESSE [A.J.C. Beliën, M.A. Botchev, J.P. Goedbloed, B. van der Holst, R. Keppens, J. Comp. Physics 182 (2002) 91], which discriminates between the different elliptic flow regimes that may occur. PHOENIX makes use of a finite element method in combination with a spectral method for the discretization. This leads to a large generalized eigenvalue problem, which is solved by means of Jacobi–Davidson algorithm [G.L.G. Sleijpen, H.A. van der Vorst, SIAM J. Matrix Anal. Appl. 17 (1996) 401]. PHOENIX is compared with CASTOR, PEST-1 and ERATO for an internal mode of Soloviev equilibria. Furthermore, the resistive internal kink mode has been computed to demonstrate that the code can accurately handle small values for the resistivity. A new reference test case for a Soloviev-like equilibrium with toroidal flow shows that, on a particular unstable mode, the flow has a quantifiable stabilizing effect regardless of the direction of the flow. PHOENIX reproduces the Toroidal Flow induced Alfvén Eigenmode (TFAE, [B. van der Holst, A.J.C. Beliën, J.P. Goedbloed, Phys. Rev. Lett. 84 (2000) 2865]) where finite resistivity in combination with equilibrium flow effects causes resonant damping. Localized ideal gap modes are presented for tokamak plasmas with toroidal and poloidal flow. Finally, we demonstrate the ability to spectrally diagnose magnetized accretion disk equilibria where gravity acts together with either purely toroidal flow or both toroidal and poloidal flow. These cases show that the MHD continua can be unstable or overstable due to the presence of a gravitational field together with equilibrium flow-driven dynamics [J.P. Goedbloed, A.J.C. Beliën, B. van der Holst, R. Keppens, Phys. Plasmas 11 (2004) 28].