For models created outside of GeneXproTools or for GeneXproTools models modified by the user, the starting model is fed to the algorithm through the Change Seed window where both the fitness and structural soundness of the model are tested.

Then, in the Run Panel, by clicking the Simplify button, an evolutionary process starts in which all the subsequent models will be descendants of the model you want to simplify. Keep in mind, however, that the simplification algorithm used by GeneXproTools is an evolutionary one and, despite parsimony pressure being applied, models continue to be selected preferentially by fitness and sometimes their complexity might even increase temporarily if the gain in fitness outweighs the loss in simplicity.

For models created in the GeneXproTools 4.0 environment, you just have to select the model you want to simplify (either the best-of-run or an intermediate model picked up in the History Panel) and then click the Simplify button and let the algorithm create better descendants not only in terms of fitness but also in terms of size. This can be done for as long as you wish or until you feel the program is as parsimonious as it will get. By monitoring the plots Avg/Best Size and Sub-Program Sizes as well as the Heat Map in the Run Panel, you will know exactly how the simplification process is progressing.