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Gephi is an open source program to explore network graphs and node and link diagrams. The program helps identify clusters, algorithmically arranges the network for readability, and helps visualize change over time. The program also lets you customize the view with colors, labels, grouping, and filtering.
What you'll need:
No programming needed but Java required
Accepted file formats:
License: Open source
Cytoscape is a Java-based open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps / plugins.
NodeXL Basic is a free, open-source template for Microsoft® Excel® 2007, 2010, 2013 and 2016 that makes it easy to explore network graphs. With NodeXL, you can enter a network edge list in a worksheet, click a button and see your graph, all in the familiar environment of the Excel window.
igraph is a collection of open-source network analysis tools with the emphasis on efficiency, portability, and ease of use. The igraph network-analysis package can be used with R, Python, C/C++.