Click on the Genomic alignments (image) in any Gene tab and select an alignment to view the pairwse alignment for the two species in that region. Or click on Genomic alignments (text) to view the text display of the pairwise alignment. Links at the left of the Gene tab also provide access to Gene trees (image and text), orthologues and paralogues.
Graphical views showing multi-species comparisons are also available in the Location tab. The Alignments (image) view displays genomic alignments, including genes present in the pairwise alignments (you need to select the alignment to be displayed). The Region comparison view shows genomes from multiple species side by side (you need to select all the species you want to add to the Region comparison view). A dedicated Synteny view is also available in the Location tab.