MaxAlign outputs an alignment in FASTA
format. This alignment contains only a subset of the sequences you have provided to MaxAlign.
Under MaxAlign alignment
you have a report on how much better your alignment became, in which you can compare the alignment area before and after the MaxAlign run . You can also see how many sequences were excluded and included, and follow the links to see which ones.
In case you have clicked on Detailed output
you will have access to the details of the MaxAlign iterative run, seeing which sequences were excluded at which stage.
And if you have provided a second alignment, you will get your output based on that alignment, and not on your first alignment. For example, you can provide a nucleotide alignment as the second alignment, and the translation as the first alignment. Computations will be done on the first alignment, but the output will be printed as a nucleotide alignment.