Here's my first attempt at a web pages documentation. This one is for the Golden Gate Assembler tool. Let me know what you think. jorgensen.biology.utah.edu/wayned/ape/D...

I want to make more helpful how-to's for ApE. What format do you like to see this kind of information in? A PDF? A set of web pages? Bluesky threads?

I just uploaded version 3.1.7. This update fixes a bug that caused failure to recognize some substrates in the Recombination reaction tool. Also the first full version with the option of inline feature display (option in the preferences). Fixed other bugs too