The documentation presented in this report includes brief listings of the methods used and detailed descriptions of the required input files and typical use of the output files. Detailed information on the methods, guidelines for conducting sensitivity analysis, data needs assessment, calibration, and uncertainty evaluation of a model of a complex system using examples mostly from ground-water modeling, and well-documented instructional exercises are presented by Hill and Tiedeman (in press). Together, this report, Hill and Tiedeman (in press), and Christensen and Cooley (2005) serve to document the computer codes described in this work. A more limited discussion of most of the methods and a previous version of the guidelines are presented in Hill (1994) and Hill (1998), which served to partially document the earlier programs. More on the methods described by Christensen and Cooley (2005) is presented by Cooley (2004).