A large number of alignment statistics and properties are computed in order to facilitate their comparison. Additional alignments can be uploaded and integrated in the comparison.
If you want to compute your alignments locally, the stand-alone alignment programs can be downloaded here.
If you find CSA useful for your work, please cite
I. Wohlers, N. Malod-Dognin, R. Andonov and G.W. Klau. CSA: comprehensive comparison of pairwise protein structure alignments. Nucleic Acids Res, 40(Web Server issue):303-309, 2012.
Example 1: Comparing alignments and scorings and identifying common cores
Example 2: Aligning flexible proteins: one hinge residue
Example 3: Aligning flexible proteins: two hinge residues