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Table 1 Comparison of graph visualization software

From: Mango: combining and analyzing heterogeneous biological networks

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
  1. 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