Yes, using Cointegration is an option in the software and we use it as a critical component of our trading system, though that is a choice. By default Cointegration is toggled off when you install PTF PRO as it is computationally costly. To enable it you will need to go to System Preferences by clicking the top left “pear” button, and then enable co-integration. Also note that it's calculated on end-of-day data.