Figure 2

Pairwise viewing mode. In this viewing mode, conserved regions are shown between adjacent genomes. Genomes can be rearranged, removed, or shown more than once. Clicking the “Optimize order” button at the top rearranges the genomes to show more associations with fewer total genome tracks. Genome control panels on the left side of the interface allow the genome viewing ranges to be adjusted. Master controls at the top apply to all genomes. If an optional annotation input file was provided, then one annotation track will be shown within each genome track. Using the control panel on the left, users can choose the visible annotation track as well as the shape and color of the annotations. Visible synteny regions can be filtered based on numerical criteria specified for each region in the synteny input file. See main text for more details.