The Multi-Model Analysis (MMA) computer code is designed to evaluate many alternative models of a given system, called multiple models in this work. It can be used to rank the models and calculate posterior model probabilities. The probabilities are used to calculate modelaveraged quantities that account for the variability evident in the alternative models. The modelaveraged quantities can include parameter estimates, predictions, and measures of parameter and prediction uncertainty. Calibration of all models needs to be completed before application of MMA. MMA operates by reading files produced by models developed and calibrated to represent a single system. The models all need to use the same observations with the same weighting. The files needed by MMA can be produced by UCODE_2005 and associated codes (Poeter and others, 2005) run in the Sensitivity-Analysis or Parameter-Estimation mode. The name and structure of the files are simple and follow the conventions of JUPITER API data-exchange files. Thus, it is likely that MMA also will be able to use results from codes other than UCODE_2005. Although the examples presented in this work are from the field of groundwater modeling, MMA (and UCODE_2005) can be used to evaluate results from models of nearly any type of system. The documentation presented in this report describes the methods used and the input and output files. Together, this report, Hill and Tiedeman (2007), and Burnham and Anderson (2002) serve to document the computer code described in this work. Additional information on the methods is provided in Burnham and Anderson (2004), Ye and others (2004, 2005), and Poeter and Anderson (2005). The performance of MMA has been tested in a variety of applications. Future applications, however, might reveal errors that were not detected in the test simulations. Users are requested to notify the originating office of any errors found in the report or the computer program. Updates might occasionally be made to both the report and the computer program. Users can check for updates on the World Wide Web at URL