Sequence data normally need's a lot of memory. To be able to handle thousands of sequences we implemented an online compression. All data is compressed most of the time and only uncompressed on demand. As a user you only find smaller database files, that's all. Without understanding the data, the program can compress data only by a limited factor. With the help of a tree aligned sequences can be compressed much better by storing only the differences to a consensus sequence. Once a sequence is compressed using a tree, it will keep the good compression method until it is changed. Then only the older method is used. As long as you change only a few (up to 100) sequences, the database won't grow very much.
To compress the entire database, the program needs a tree, which should cover most of the sequences. The larger and better the tree, the better the compression.