SPheno 3.1 is an updated version of the program that includes extensions for flavor, CP-phases, and models beyond the Minimal Supersymmetric Standard Model (MSSM). The program calculates the masses and couplings of supersymmetric particles in various models, including those with generation mixing and CP-violating phases. It also includes the calculation of low energy observables and extends the SUSY Les Houches Accord (SLHA) for these models. The program uses the Runge-Kutta method to solve the renormalization group equations and includes the calculation of decay widths, branching ratios, and cross sections for supersymmetric particles in electron-positron annihilation. It also calculates low energy constraints in the B-meson sector, such as BR(b→sγ), ΔM_Bs, rare lepton decays, and SUSY contributions to anomalous magnetic moments and electric dipole moments. The program supports various models, including seesaw mechanisms, and allows for the inclusion of R-parity violation. It also includes new input blocks for specifying model parameters and new output blocks for low energy observables. The program is designed for use on Linux-based systems and can be compiled with various compilers. The program is continuously being developed to include additional models and low energy observables.SPheno 3.1 is an updated version of the program that includes extensions for flavor, CP-phases, and models beyond the Minimal Supersymmetric Standard Model (MSSM). The program calculates the masses and couplings of supersymmetric particles in various models, including those with generation mixing and CP-violating phases. It also includes the calculation of low energy observables and extends the SUSY Les Houches Accord (SLHA) for these models. The program uses the Runge-Kutta method to solve the renormalization group equations and includes the calculation of decay widths, branching ratios, and cross sections for supersymmetric particles in electron-positron annihilation. It also calculates low energy constraints in the B-meson sector, such as BR(b→sγ), ΔM_Bs, rare lepton decays, and SUSY contributions to anomalous magnetic moments and electric dipole moments. The program supports various models, including seesaw mechanisms, and allows for the inclusion of R-parity violation. It also includes new input blocks for specifying model parameters and new output blocks for low energy observables. The program is designed for use on Linux-based systems and can be compiled with various compilers. The program is continuously being developed to include additional models and low energy observables.