Comparison of TC Scores for default and ML tree. TC scores for default tree along x-axis, for phylogenetic tree along y-axis for (a) Clustal Omega, (b) MAFFT FFT-NS-i, (c) MAFFT L-INS-i, (d) MUSCLE. Colour dots are used for individual protein families: Blue and green for high percentage identity reference alignments, yellow and red for low identity. Black box is used for average TC score. Below the dotted line the default tree is better than the ML tree, above the ML tree is better than the default tree.