Phylogenetic compatibility matrix of tomato-infecting begomovirus sequences, exhibiting frequencies of phylogeny violations for each pairwise comparison of sequence fragments. For this analysis sequence fragments of 300 bases and 100 base intervals were used. Phylogeny violations above the threshold bootstrap value of 70% are shown. Frequencies are color coded to indicate number of phylogeny violations per sequence. The genome map drawn to scale has been superimposed to indicate the positions of genes in DNA A sequences. Positions were drawn relative to the ToLCGV-[Var] strain.