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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

Click here to download source code.