Hey there, I made a few changes to the bingo class in LeMone, to take into account the multiple module sets that are now generated by the program. All you need is to have in your current directory the bingo_gui.properties file and a BiNGO directory containing the GO and annotation files (or a link to those files). The class will then generate a bingo_results directory containing the .bgo files for each module of each module set. See the javadoc or the class for details. Changes are in the svn repository. -- Eric