beside sequences count and average length limit for the alignment stage there is also a limitation on the phylogeny stage (sequences_count*sequences_count*aligned_sequence_length=80000000) that will be checked once the alignment is done.
usual bootstrapping procedure is replaced by a new confidence index that is much faster to compute.
See Anisimova M., Gascuel O. Approximate likelihood ratio test for branchs: A fast, accurate and powerful alternative.
Syst Biol. 2006, Aug;55(4):539-52. (PubMed
) for details.