The input to the SE is two superimposed structure files, in either PDB format, ASTRAL domain ent format or SHEBA env format. If the structure contains non-standard residues, these are translated to standard ones according to the translation table on the ASTRAL Web site at http://astral.berkeley.edu/raf.html.
The default output is the sequence alignment on the screen. Aligned residues are in Upper case while unaligned ones are in lower case. The secondary structure information of the sequences is shown in different colors: red for alpha-helix, green for beta-sheet and blue for turns. It also gives statistics of the alignment including:
-fasta to show the statistics and the alignment in FASTA format on screen as well as in a file PDB1-PDB2.fasta.