Dot is open source at https://github.com/marianattestad/dot.
On DNAnexus, the featured project MUMmer + Dot contains a kit of things to get started with:
- An Applet for running MUMmer's nucmer aligner that includes DotPrep.py
- A shortcut to Dot that automatically creates the necessary access URLs for your files stored on DNAnexus
- Example initial data and results of the Applet, ready to use in Dot
If you cannot make a free DNAnexus account, then just download the DotPrep.py
script and run it on the output from MUMmer's nucmer aligner, which will give you the same results as the Applet on DNAnexus.