Sum Of Pairs Score
The "Sum-of-Pairs Score" is an accuracy metric for a multiple alignment relative to a reference alignment, based on the number of correctly aligned residue pairs summed over all pairs of sequences.
The accuracy metric can equivalently be viewed as a similarity metric between two multiple alignments.
This metric was used by the Bali Base benchmark.
- Thompson et al.: BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics 1999;15:87-8.