You can set the preferences for Synorth in the Preferences page. For example the image width, which reference and compared species to show, the appearance of the tracks, which ortholog set to use etc.

Here is a screenshot for the Preferences page, along with brief explanations of the various options found there:

A.	Gene coverage threshold The synteny block as defined by the joinedNet strategy (see Methods) may cover only a part of a gene. This is especially common for short genes at the edge of the synteny block. The inclusion/exclusion of any gene is based on the fraction of the gene covered by the synteny block. The default percentage threshold is 30%, which means a gene is included into the GRB only if it has at least 30% length overlapping with the joinedNet.
B.	Ortholog set One ortholog set, which is Ensembl ortholog (v49) is provided with two options: * Option1: plus the un-annotated ortholog predicted by the exonAligned method with criteria (alignedDNA>50% or alignedExon>10 or alignedExon/totalExon>50%)(see methods for details). * Option2: exclude the out-paralogs (see method for details).
C.	Reference/compared species At present, only human genome is available as a reference species. More options will be provided in future versions.
D.	Image Configuration You can change image width (in pixels), as well as toggle the display of gene names, HCNEs, and the "link line" between genes.
E.	Track display option Hide/open all tracks, or use the Smart mode. The smart pack mode allows display of tracks with 1) more than 10 HCNEs, 2) chromosomes containing at least half of the GRB gene orthologs, 3) chromosomes that harbor the transcription factor ortholog, and/or 4) chromosomes that harbor the putative target gene.