SOFTSUSY is a program designed to accurately calculate the spectrum of superparticles in the CP-conserving Minimal Supersymmetric Standard Model (MSSM) with full flavor mixing. The program solves renormalization group equations, incorporating theoretical constraints on soft supersymmetry breaking terms provided by the user. It uses weak-scale gauge coupling and fermion mass data, including one-loop finite MSSM corrections, as boundary conditions, and can also calculate a measure of fine-tuning. The program is structured to be easily generalized to extensions of the MSSM. This article serves as a comprehensive guide for prospective users, detailing the conventions and approximations used. The program can be run using either the SUSY Les Houches Accord format or command-line arguments, and it is available for free from the SOFTSUSY web page. The article covers the relevant MSSM parameters, the algorithm for performing the calculation, and provides technical information on running and extending the program.SOFTSUSY is a program designed to accurately calculate the spectrum of superparticles in the CP-conserving Minimal Supersymmetric Standard Model (MSSM) with full flavor mixing. The program solves renormalization group equations, incorporating theoretical constraints on soft supersymmetry breaking terms provided by the user. It uses weak-scale gauge coupling and fermion mass data, including one-loop finite MSSM corrections, as boundary conditions, and can also calculate a measure of fine-tuning. The program is structured to be easily generalized to extensions of the MSSM. This article serves as a comprehensive guide for prospective users, detailing the conventions and approximations used. The program can be run using either the SUSY Les Houches Accord format or command-line arguments, and it is available for free from the SOFTSUSY web page. The article covers the relevant MSSM parameters, the algorithm for performing the calculation, and provides technical information on running and extending the program.