Anagram generation is divided into four stages. These stages are indicated by the four large buttons that appear on the left of the main window at all times:
You can move between stages by clicking on the relevant stage button. Anagram Genius will then go to this stage doing just enough work to get there. For example, if you are at the Word Stage and click on the Weed button, Anagram Genius will be forced to do the anagram search first. However, if you are at the Weed Stage and click on Input, Anagram Genius will take you back to the input stage immediately as no work is required to go there.
The current stage (i.e. the one that Anagram Genius is currently on) is indicated by its stage button being "lit up". The target stage (the button you have clicked on and where Anagram Genius will eventually stop) is indicated by the button being depressed. When there is no work being done, the program has come to rest and the button pressed will also be the button which is lit up.
At its very simplest, making anagrams involves entering a text at the Input Stage, clicking on the Weed button to proceed to the Weed Stage and selecting the best anagrams.
However, the list of best anagrams can be controlled and built up over several anagram runs, switching back and forth between the Input, Word and Weed stages or even done over several runs of the program. (Your efforts in interacting with Anagram Genius are automatically saved.)