Fig. 1

Example of OrthoRefine’s synteny analysis. The window around three genes assigned to HOG19 by OrthoFinder demonstrates how OrthoRefine determines which of the E. coli genes is an ortholog of E. fergusonii’s HVX45_RS11505. The HOG19 genes are shown with yellow fill, other genes assigned to the same HOG are shown in matching colors, and genes that have orthologs in other genomes outside the displayed window are shown in white. The first number below each circle denotes the HOG assigned by OrthoFinder, while the second entry shows the locus tag