We report on a new software tool, SUBTRACT, which allows the analysis of the possible strategies for an experiment based on a mathematical model of subtractive hybridization. The program helps the experimenter choose the optimal strategy and conditions for performing the reaction. The program allows the modeling of cDNA and genomic subtraction for different types of target DNA. SUBTRACT offers a friendly interface for the investigation of the dynamics of the process of subtractive hybridization, and for modifying different parameters and initial conditions. SUBTRACT allows the user to plot the values of interesting quantities as a function of the reaction time. The program runs under the Unix operating system on Sun-compatible computers.