Figure 3

Homology to X4 seed strain. For each sequence s_i the Euclidean distance to the seed sequence s _seed in the probabilities plane (Figure 2) is given on the vertical axis, while the horizontal axis shows the "alignment distance" to the seed sequence given by (1 - A(s_i, s _seed ))/(A(s _seed , s _seed )) with sequence alignment score A based on Needleman-Wunsch alignment [23] with scoring matrix BLOSUM62 [24]. The lower the alignment distance, the higher the homology to the seed strain. Sequences predicted as "X4" are orange, those predicted "R5" cyan. The seed sequence is the red point in lower left corner. The figure shows that sequences close to the seed strain in Figure 2 have also low alignment distance, i.e. are close homologs.