thanks for reading my blog I will add ApE to the list. I had used it last year. There is a really useful feature to search for restriction sites that aren’t present, which I used for inserting custom sites by directed mutagenesis. Our lab has a copy of clone manager which I’ve found to be indispensable and although I don’t normally use commercial software, it’s well worth the money. A colleague of mine swears by serial cloner as well, but I haven’t used it.

has the ability to color based on a feature list, etc etc.

good tutorial here

http://openwetware.org/wiki/Arking:JCATutorialIntro9