If you want to simply reference Grapher in the body of the paper, you could use "GrapherTM 12 from Golden Software, LLC (www.goldensoftware.com)" or "GrapherTM 12 (Golden Software, LLC)". Grapher is trademarked, and so it has a TM after it.
If you want to reference Grapher at the end in a bibliography or reference list, our information is:
Golden Software, LLC.
809 14th Street
Golden, Colorado 80401
Updated September 29, 2016