Matrix names are the same as in Table 1. Abbreviations: FSM-SUP - family-specific matrices tested on groups from the SUP sub-set. FSM-TWI - fold-specific matrices tested on groups from the TWI sub-set. Adaptive FSM-SUP - the adaptive family-specific matrix selection procedure tested on the groups from the SUP sub-set. The results shown are for groups with 10 or more reference alignments (244 groups in the SUP sub-set, 131 groups in the TWI sub-set). A cell formed by the intersection of row i and column j shows the results of the pair-wise comparison of matrices (i, j), and contains two numbers: first is the number of groups on which matrix i performs significantly better than j, second is the number of groups on which matrix j performs significantly better than i.