Gibthon Construct Designeris a software tool under active development to aid with the design of primers for Gibson Assembly. It currently comes in two flavours - Gibthon Beta, and Gibthon Construct Designer Beta. The software is released under the BSD license, and the source code can be obtained for either by email
Gibthon Beta - here
The developer is currently focussing on GCD, but will still be supporting Gibthon - contact him here
Gibthon Construct Designer Beta - here
Generating the primers for PCR extension takes only a few seconds each, and the information is returned to the user in the form of a PDF with a datasheet for each primer. In the near future it will also provide all the necessary protocols to complete your construct. As time goes by, more granular conrol over settings will become available.
The algorithm for optimising primer length is still under development, so should not be entirely trusted until the software comes out of beta. When you find something that doesn't work, or could be improved, please email the developer.
How it worksFor the latest information on what algorithms Gibthon uses for generating primers, please check the site as this wiki might be a bit behind. There is also a video demo you can watch here on how to use it: