It depends on what you want to pay and what you wnat to do.
GENERUNNER and DNAMAN are reasonably good and not too expensive. The
latter is better at graphical output, but not as good at analysis.
For simple things there is a lot of freeware available, and many thins
can be done on the Web. For heavy duty work (espec. sequence
assembly) I think Lasergene from DNASTAR is really the only
alternative, but is very expensive.
I have contact numbers if you are interested.
Peter J. Myler phone: (206) 284-8846x332
Seattle Biomedical Research Institute FAX: (206) 284-0313
4 Nickerson Street e-mail: MYLERPJ at U.WASHINGTON.EDU
Seattle, WA 98109-1651