ConGENER is a software package for combinatorial generation and characterization of molecular libraries containing substitution isomers, so called congeners. The molecules are built by substituting hydrogen atoms in the parent molecule with a combination of desired atoms. The ConGENER program is described in Sections 2-5. The scripts to run QM calculations are described in Section 6.ConGENER has been written in standard C++.Requirements:· g++INSTALLATION:To compile under any common Linux/Unix distribution, just type:g++ congener. cpp –o congenerIn order to use the program, execute the „congener" binary.The program runs in the interactive mode asking user a number of questions about the geometry of the parent molecule and isomer space to be expanded. However, to facilitate running multiple jobs or restarting, all answers can be combined as one input file. In order use the passive mode and read the input file use:./congener < input_fileThe information how to prepare input data for ConGENER is described in the following sections of this manual.