Calculation of alignment score for the inferred ancestral monocot and eudicot sequences of the psbK gene.

The ancestral sequences for the monocots, and the eudicots, are inferred independently, and then the alignment scores calculated in the program MUSCLE. The individual column scores depend on the frequencies and properties of the two amino acids; higher scores are given for pairs that are similar (readily substitutable) or specific (more readily substitutable for each other than for other amino acids). The column scores are summed to produce the alignment score.