This is a quality scoring program that compares two multiple sequence alignments: an alignment to be evaluated (the ”test” alignment) and a second alignment that is believed to be correct (the ”reference” alignment). The program outputs the following scores: The PREFAB Q score (aka the Balibase SPS score or the Developer score). The Modeler score. The Cline et al. shift score. The Balibase TC (total column) score.