An App for CytoScape that allows users to view SANA alignments(https://github.com/nmamano/SANA/tree/SANA2/src)
To use this in CytoScape, you first need to use IntelliJ and Maven to build the project with Java 8. You can find a really good tutorial to do this through this video: https://www.youtube.com/watch?v=Y0jhySTHwN4. Then, you can load the .java file as an app inside of CytoScape.
To use, find the VisAl submenu under the Apps menu. To create the graph, use the Draw Alignment from Files option to specify two graph files and an align file. The first graph file should be the larger network. From here, the other options will have effects on the graph created by VisAl. When the graph is created, all the points are grouped onto on point, thus, you need to apply a layout of your choice from the layouts menu. The other options under the VisAl submenu should be self explanatory. You can select certain nodes and the edges connected to these nodes will be isolated. If the induced subgraph option is selected, the induced subgraph between the nodes will be shown.