The second page of the server allows you to select the query you wish to perform on your data. Here is a screenshot with explanation of each part.
Follow steps A - B for whole genome analysis.
Step A: Select the reference genome; genome rearrangement in all other genomes will be shown in reference to this genome.
Step B: Click on "Submit Query" to proceed.
Follow steps C - E for comparing one chromosome with another.
Step C: Select the reference genome and chromosome.
Step D: Select the target genome and a chromosome.
Step E: Click on "Submit Query" to proceed.
Follow steps F - H for finding synteny around a marker.
Step F: Select a genome.
Step G: Enter the symbol of a gene/marker on that genome. For pre-loaded data, use the official symbol. For your own data, enter the same symbol as used in the data files.
Step H: Click on "Submit Query" to proceed.