The default limit max number of sequences you can load is 3000 but it can be easily increased by editing .icm/config/icm.cgf file located in your home directory
See
http://www.molsoft.com/man/files.html#icm.cfg
Once sequences are loaded (double click on sequence folder in the ICM workspace to select, then right click and choose 'Align') you can display alignment tree side-by-side with the alignment.