The AGILE Science Tools are written in C++ and are based on the ROOT (CERN) and CFITSIO (NASA) libraries. All the tools can be run from the command line. The Science Tools use the Parameter Interface Library (PIL), developed by the ISDC, for parameter input, allowing a variety of input methods: 1. the user can input all or some of the parameters on the command line, in the same order as the provided parameter file; 2. the user can start the tool, which then asks for the values of some parameters interactively on the console; 3. by adding ’mode=h’ on the command line, the user can accept all the defaults (the last values used) for parameter values not explicitly provided on the command line The input and output files are in FITS format. FITS files consist of a series of units, each containing a header and data. Each header contains a list of ’keywords’ and their values, which describe the format of the data. The first unit is the ’primary’ unit and may or may not contain data. The subsequent units are called ’extensions.’ FITS files can be read and modified by standard tools such as fv and the output maps generated by the tools can be displayed with the ds9 tool.