Fig. 8
Overlap between genomic regions of different genes may complicate the inference of gene orthology. In each subfigure, genomic regions of two genes in one genome overlap strongly with each other, and all non-nested maximal matches shared with a certain gene in the other genome are found within the overlapping region. Without inferring the evolutionary histories of these genes via outgroup genes, automated sequence comparison alone is not able to distinguish those pairs of genes that are actually primary orthologous