A collection of tools for designing and manipulating DNA sequences is offered on the Gene Design website at Johns Hopkins School of Medicine. The authors are not clearly identified on the website, but New Scientist reported that:
GeneDesign was created by researchers led by Jef Boeke at Johns Hopkins University School of Medicine in Baltimore, US.
This set of tools for designing and analyzing DNA sequences and for selecting restriction enzymes and vectors has a few features I find appealing in software: university-developed, web-based, free, and open-source. Several similar resources were suggested on Slashdot.