Fig. 4

Proportions of three broad score categories. Each pie chart shows the proportions of 3 broad score categories, I (magenta), D (cyan) and S (yellow), in a particular MSA set (row) via a specified alignment method (column). The specific “progressive” and “iterative” options of MAFFT are E-INS-1 and E-INS-i, respectively. For the definitions of the 3 categories, see Fig. 3. For numerical values of the proportions and the absolute frequencies, see Additional file 1: Table S2