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Note: This is the documentation for SynMap3D, if you are looking for SynMap 2 look here.


SynMap3D is a web-based whole-genome synteny browser that both identifies and visualizes regions of synteny (common ancestry) between three genomes. Results are displayed as a three dimensional dotplot (scatter plot), with each axis representing a linearized version of the genome. Alternating light/dark axis colors and grey grid lines distinguish between different chromosomes. Each point represents a syntenic gene pair shared between all three genomes.

Getting Started

Coming Soon!

Understanding the Results

Coming Soon!


Human vs Chimp vs Orangutan: [1] A. thaliana vs A. lyrata vs B. rapa: [2]


How can I use VR-mode?
VR-mode requires both a VR-compatible web browser and a VR headset. For information on setting up a VR-compatible browser, please visit
What web-visualization technologies are used in SynMap3D?
The three-dimensional dot plot is rendered with WebGL using Three.js. Histograms are pure D3.
How many points can SynMap3D support?
This really depends on the individual user's system, but we have been able to render well over 50K points with good performance.
How can I reduce the number of points displayed?
There are two steps at which point number can be reduced: pre-visualization (through the wizard options) or post-render (by selecting histogram regions). During the wizard step, the four general options "Minimum syntenic points per contig", "Minimum contig length (bp)", "Limit by mutation value", and "Limit by DBSCAN clustering" can all be used to reduce point count (see 'Getting Started' for detailed information about each option. After rendering, data can be subsetted by selecting a region of the histogram. The visualization will live-update to display only the points falling within those values.
Is SynMap3D open source?
Absolutely! All CoGe tools are open source and can be viewed at our team's GitHub repository ( If you are specifically interested in SynMap3D, most of the visualizations are controlled by the javascript files in web/js/syn3d.
Question not answered here?
Feel free to contact Asher @ ahaug (at) email (dot) arizona (dot) edu