It combines its own knowledge with the description of the input text that you gave it to assign scores to the individual words. This information is used later during anagram generation. These scores can be changed manually so if you see words that are especially relevant to the input text you can boost their score and the software will make an extra effort to use them in the resulting anagrams. If you want a complete list of these words they can be saved or printed out. The Search Stage is where it finally searches for anagrams scoring them according to what it understands to be their likelihood to be relevant and make sense.
Some longish phrases have literally millions of combinations of words that form anagrams.
Anagram Genius's scoring system means that you only have to hand search through a small selection to find the gems. Finally the Weed Stage is where the user scans through the output and selects the best anagrams for saving or printing out in a report. The user also has the option to change the word order and punctuation at this stage. The report also includes some extra things such as the longest single words found.