The Primer features in Geneious Prime are based on a modified version of the program Primer3 (http://bioinfo.ut.ee/primer3/).
Copyright (c) 1996,1997,1998,1999,2000,2001,2004 Whitehead Institute for Biomedical Research. All rights reserved.
A copy of the modified Primer3 source that Geneious Prime runs is distributed with the plugin.
If you use the primer design feature of Geneious Prime for publication we request that you cite Primer3 as:
Steve Rozen and Helen J. Skaletsky (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386 Source code available at http://sourceforge.net/projects/primer3/.
Further information on the functionality of the primer design feature can be found in the primer3 documentation available here: http://primer3.ut.ee/primer3web_help.htm. Please note that some controls have been changed, renamed or removed from Geneious, but most of the primer3 functionality is available.