In another effort to make more webbyscience, I've been rewriting Paul Stothard's Sequence Manipulation Suite into a single-paged, modular, dynamic web application. Only the 'Codon Plot' function is working so far, but feel free to give it a try.
It'll probably only work in the most recent Mozilla-based browsers (i.e. not IE or Safari), as it's using E4X for some of the functions.
The original is GPL-licensed, and this will be too once I've got all the pieces into place.