A detailed synteny view in Apollo showing part of human chromosome 20 at the top and part of mouse chromosome 2 at the bottom is illustrated. In the middle are links between orthologous genes as identified by the Ensembl synteny-generating software. The links are crossed because the genes in the top panel and in the bottom panel are in different orientations on their respective chromosomes. Although this figure only shows gene links, other types of link may also be displayed. Information about the genes from both genomes are read from Ensembl databases and information about orthologous gene pairs can either be read from an Ensembl compara database or from a flat file. The central panel can be used to scroll back and forth along the syntenic region or to center the display on a particular region by clicking on one of the colored matches. The top and bottom Apollo panels behave just as a normal, single Apollo panel and can be zoomed, scrolled, collapsed and also link out to a web page (as configured by the user).