You can mark lines on which you want to stop under debugger with breakpoints. There can be unlimited number of breakpoints in various analysis techniques at the same time. When one of the breakpoints will be reached calculation of analysis technique will be stopped and you will see debugger window with the breakpoint line selected. At this time you can add/remove breakpoins, step through analysis technique code, watch variable's values or continue execution of analysis technique.
See also Debugging Analysis Techniques.