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View Code? Open in Web Editor NEWSWAlign.jar is a simple and robust alignment program for protein sequence-to-sequence alignment based on the standard Smith-Waterman dynamic programming algorithm. The mutation matrix is from BLOSUM62 with gap openning penaly=-11 and gap extension panalty=-1. The program is written by Renxiang Yan at Dr. Yang Zhang's laboratory in the Univerisity of Michigan. Small modifications were made to display residue mapping and output a json object.