Could you expand what you mean by comparing?
As @dick_freebird says, you can do polygon comparison with some scripts. DRC check would be one of them. You could also build your own tcl/skill script to compare each rectangle paint of one design against another design. Think of it as "moving" the mouse automatically to each polygon and checking if the polygon exists in both designs at the same coordinates. I did a bunch of those scripts for short-circuit detection, but I used a little-known GDS tool named: Micromagic. But it is definitely possible to do this in virtuoso too.
For functional comparison, you would perfrom LVS and compare to a golden or schematic netlist. @dick_freebird mentioned Assura, but there are anothe programs like Mentor Graphics Calibre, etc.
For performance comparison, you want to extract the netlist and run spice simulations. that will tell you what the differences are in timing due to parasitic capacitances and resistances.