Dayhoff matrix comparisons. Elements of leaf-leaf (x-axis) and node-node (y-axis) Dayhoff matrices are plotted together from (A) short, (B) medium and (C) long branches. The coefficient of determination calculated by linear regression is shown. Labeled points involve the amino acids alanine or valine. The all fractional counting method was used in node-node comparisons shown. Similar results were obtained with the other counting methods (data not shown).