Gephi and Cytoscape (https://cytoscape.org/) are both open-source Java-based network analysis and visualization software.
Cytoscape.js is a graph theory and network visualization Javascript library. It can be compared to SigmaJS (http://sigmajs.org/) or the more generic D3 data visualization toolkit (https://d3js.org/).
Cytoscape.js is MUCH more capable than those, it can do client side network algorithms (A* etc) and traversal, Sigma & D3 are 'just' visualisation tools, where Gephi is an 'offline' tool
Cytoscape.js is a graph theory and network visualization Javascript library. It can be compared to SigmaJS (http://sigmajs.org/) or the more generic D3 data visualization toolkit (https://d3js.org/).