Navigation
The browser has familiar navigation interface. At the top of the window there is a navigation bar that allows you to enter a specific genome coordinates. The genome to adjust can be selected from the drop down menu. Similar to the UCSC genome browser, the first textbox allows entry of gene by name or specific coordinates. A second text box displays the coordinates of the currently displayed window.
Using the query box you can set the viewed coordinates for each genome by specifying an explicit range to be viewed (as depicted above) or by searching for features in loaded annotation files. For example, to search by gene-name, type the gene name into this box, and the browser will suggest matching features as shown below:
Using the mouse one can re-center the viewed window by clicking on a single position, as below:
Similar to existing genome browsers, you can zoom in on a slice of the current view by using a mouse drag gesture to select the coordinates you would like to zoom in on:
Zoom buttons allow the displayed segment to be zoomed in and out:
In some instances the orientation of gene is flipped between two Genomes. In this case, the 
button can be used to invert the frame of reference, so that chromosomal coordinates are displayed in decreasing order from left-to-right.
Once pairwise alignment have been loaded (see Configuration instructions ) the liftOver functionality will be enabled from the Navigation menu:
You will be presented with the following prompt:
The toggle box at the top of this window allows you to select the direction of the liftOver. In the above example we have selected dm3 -> droYak2 which means that liftOver will use the alignment and the coordinates of the view for the dm3 genome to set the coordinates in droYak2 genome. In this case the viewed segment of the dm3 genome maps to two different contigs in droYak2, so you are presented with a list of alternative choices.