"2.3 Large alignments
If you have a large number of sequences (a few thousand), or they are very long, then the default settings of may be too slow for practical use. A good compromise between speed and accuracy is to run just the first two iterations of the algorithm. On average, this gives accuracy equal to T-Coffee and speeds much faster than CLUSTALW. This is done by the option –maxiters 2, as in the following example.
Just like fishgolden stated, the alignment should have come before concatenation. I am not sure if Alignment before concatenation and after concatenation would produce the same super-matrix. I once did but I opted for before concat and I think it has a higher level of certainty compare to aligning a huge and long sequences, which would definitely be prone to error