Table 1.
Comparison of graph visualization software
| Software | Code | Graph analysis features | Visualization | Limitations |
|---|---|---|---|---|
| Cytoscape | Java | · Many algorithms for systems biology | · 2D predetermined layout | · Can only merge 2 graphs at a time |
| (v. 3.2.1) | · Can add GO or KEGG attributes | · 3D predetermined layout (via plug-in) | · 6 min to load a network with 4 M links | |
| · Plug-ins available | · | but no visual afterward | ||
| Gephi | Java | · Intuitive graph statistics | · 2D and 3D layouts but graphs cannot be | · Cannot display multiple graphs on one |
| (v. 0.8.2) | · Automated graph algorithm citation | rotated in 3D | screen | |
| · Generalized for all types of graphs | · Graph layout animation helps maintain | · Limited by JVM constraints; cannot load | ||
| · Plug-ins available | mental map | a network with 4 M links | ||
| GUESS | Java | · GYTHON, a language for graph analysis | · 2D layout only | · Cannot be run on MacOS 10.9, Windows |
| · Can map information attributes to visual | · Update with user commands | 7, or Redhat Linux 6.0 | ||
| attributes | ||||
| Graphviz | C | ·No graph analysis capabilities | ·Rich set of predetermined 2D layouts | ·Not an interactive system |
| · Streamlined command line interface | · Cannot efficiently handle graphs over | |||
| 100 nodes | ||||
| Neo4j | Java | ·Graph database system | ·Relies on JSON for visualization | ·Designed as a backend to database sup- |
| (v. 2.1.7) | · Cypher graph query language | · 2D layouts only | port rather than for visualization | |
| · Queries are based on a combination of | · Have to click a node or link to see its | · Nodes are only labeled by numbers | ||
| topology and attributes | attributes on a separate panel | · The whole database is one huge graph | ||
| Tulip | C++ | · A set of C++ libraries for graph analysis | · 2D visualization | · More useful to users who program C++ |
| (v. 4.6.1) | · Can also be run as stand-alone program | · 3D is available through plug in | or python directly | |
| · Plug-ins can be created in Python | · Had some 3D layout algorithms | · More analysis than visualization features | ||
| NetworkX | Python | · Python module for graph analysis | · Must export to other software or | · Useful only as an analysis tool |
| (v. 1.6.1) | · Rich set of network algorithms | modules for visualization | ||
| Mango | C++ | · Provides general graph mathematics | · Interactive 3D layouts and controls | · Does not yet have plug-in feature |
| (v. 1.10) | · Heterogeneous graph analysis with ease | · Real-time large graph visualization | · Does not yet use GPU speedup | |
| · Takes ∼30 s to load a 4M link network | · User customizable visual attributes | · Limited set of preset layouts |
Benchmarks were performed on a 2010 Mac mini that has 8 Gb RAM and runs 64-bit MacOS X 10.9 with a 2.4 GHz Intel Core 2 Duo processor. All software were run using their default configurations