The normal MULTALIGN program is limited to up to 500 sequences not exceeding 1200 amino acids length. As a consequence, the maximum sequence length considered in a database scan is also 1200. Sequences of greater than 1200 amino acids in length will be IGNORED. The program reports how many sequences were actually compared in the scan at the end of the output file.
IMPORTANT: THE AMULT PROGRAM MUST HAVE BEEN RECOMPILED FOR LONG SEQUENCES TO USE THIS OPTION. THIS IS NOT THE DEFAULT INSTALLATION. PLEASE SEE THE NOTES IN THE FILE CALLED BUILD.