Table 1. Summary of network visualisation tools commonly used for the analysis of biological data.
| Graph Type Specialism | Scalability (graph elements) [1] | Layout Dimension | Layout Algorithm | Static or Dynamic Layout |
Clustering | Transforms | File Formats Supported | Under Active Development | License | |
|---|---|---|---|---|---|---|---|---|---|---|
| Cytoscape | Knowledge-based | ~100,000 [2] | 2D [3] | Various | Static | Various [4] | Various (via 3rd party plugins) [4,5] | GML, GraphML, BioPAX, Excel, CSV/TSV, SIF, SBML, XGMML, NNF, PSI-MI, CX/CX2 | Yes | LGPL 2 |
| Gephi | General | ~300,000 | 2D | Various | Dynamic [6] | Girvan-Newman and Leiden [3] | Network Diameter, Graph Density, HITS, Modularity, PageRank, various others [4] | GML, GraphML, UCINet, DOT, GDF, GEXF, Pajek, TGF, TLP, VNA, CSV/TSV | No | CDDL/GPL 3 |
| Tulip | General | ~10,000 | 2D | Various (mostly OGDF) | Static | MCL, Louvain, Convolution, Link Communities, Strength | Betweenness, Eccentricity, PageRank, Strahler, Welsh Powell | GML, GraphML, BibTeX, GEXF, JSON graph, Pajek, DOT | Yes | LGPL 3 |
| Bandage | De Novo DNA Assembly |
~10,000 | 2D | Domain Specific | Static | N/A | N/A | LastGraph, GFA, FASTG, FASTA, ASQG | No | GPL 3 |
| Graphia | Data Driven (correlation) | ~5,000,000 | 2D & 3D | Force Directed | Dynamic | MCL, Louvain | Betweenness, Eccentricity, PageRank, k-NN | GML, GraphML, BioPAX, JSON graph, Excel, CSV/TSV/SSV, MatLab, DOT, CX/CX2 | Yes | GPL 3 |
Notes
[1] Scalability, i.e. ability to render graph elements (nodes/edges) depends on available hardware
[2] Applies to rendering; analysis is more limited
[3] 3D available via Cy3D 3rd party plugin
[4] Available via 3rd party plugin
[5] Quality and scalability varies a great deal
[6] Filters are not dynamically updated