Fig. 6
From: KnotAli: informed energy minimization through the use of evolutionary information
We compare KnotAli’s performance using mutual information, \(\mathtt{MI}\), versus its performance using adjusted mutual information, \(\mathtt{MIp}\). For each family we present the average F-measure obtained when we used (1) MUSCLE as aligner, and \(\mathtt{MI}\) to find conserved base pairs, presented with MI-MU as the leftmost bar in the figure for each family; (2) MUSCLE as aligner, and \(\mathtt{MIp}\) to find conserved base pairs, presented with MIp-MU as the second bar from the left in the figure for each family; (3) MAFFT as aligner, and \(\mathtt{MI}\) to find conserved base pairs, presented with MI-MA as the third bar from the left in the figure for each family; and (4) MAFFT as aligner, and \(\mathtt{MIp}\) to find conserved base pairs, presented with MIp-MA as the fourth bar from the left in the figure for each family