Clicking the 3D View button (shown left) opens a three-dimensional display of the syntenic regions (also called "blocks", shown in red) for selected chromosomes against a reference chromosome. Below is an example showing three chromosomes from Maize, Rice, and Sorghum against Maize chromosome 9.

The chromosomes to display are selected by clicking the chromosome diagrams on the left. Click the chromosome rectangle to add it to the display, click the number above a chromosome to make it the reference chromosome (note that this will clear the chromosome selection). Drag the mouse over the 3D view to rotate it, use the mouse scroll wheel to zoom in and out.

Click the 2D button to open the 2D View for the selected chromosomes.

Click the Dotplot button to open the Dot Plot View for the selected chromosomes.

Clicking the Block View button (shown left) opens a display of the synteny blocks for one organism aligned against the chromosomes of another organism. Below is an example for Sorghum against Rice.

The synteny blocks are colored by chromosome (see color key at top) and located on the target chromosome according to position and size. Click on chromosome to open a more detailed view as shown below.

Click on a block to open a detailed 2D View.

Clicking the Dot Plot button (shown left) opens a dot plot display for all chromosomes of all selected species with synteny blocks in red boxes. A popup window will appear asking for permission to run, click "ok".

Click inside the dot plot to open a larger view of the selected chromosome pair as shown below.

On this view, you may select any region with the mouse and click it to open a detailed 2D View.

The 2D View is available via the 3D View, Dot Plot and Block View displays. It allows navigation of the synteny blocks down to the individual hits and annotations.

Each individual anchor point (a.k.a. "hit", generated by MUMmer or BLAT) is shown as a brown line between chromosomes. Drag the mouse over a chromosome to zoom into the selected region. If you zoom down close enough you should see an image similar to below of a gene-to-gene alignment with hits from exon-to-exon. Right-click on each chromosome and select "Show Annotation Descriptions" to display the yellow info boxes (note that these are only visible when zoomed-in closely).

If you right-click with the mouse on either a sequence, contig block, contig, or hit region, you will get a context menu of options relevant to that region (these menus are also available from buttons at the top of the display):

For example, in the sequence menu you can toggle the annotation descriptions, and in the hit menu you can elect to show only those hits found to be in a synteny block.

Clicking the Circular Map button (shown left) opens a circular display of the synteny blocks for one organism against all chromosomes of another organism. Below is an example for Rice against Sorghum.