UGENE allows you to view a molecule in the anaglyph mode. To enable the anaglyph view open the Settings dialog of the 3D Structure Viewer and check the Anaglyph view check box.
You can modify the color settings: select one of the available Glasses colors or set custom colors, swap the colors.
The offset of the color layers can be adjusted by dragging the Eyes shift slider.
See the result the anaglyph view is applied to a molecule below:
