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Table 2 Comparison of software tools for biological network analysis

From: GraphCrunch 2: Software tool for network modeling, alignment and clustering

Software package Graph Properties #of models Graphlets Visualization Clustering GNA
GraphCrunch 2 Yes 7 Yes Yes (Results) Yes Yes
GraphCrunch Yes 5 Yes Yes (Results) No No
Cytoscape Yes 6 Limited Yes Yes No
Visant Yes 1 No Yes No No
mFinder No 3 No Yes (mDraw) No No
MAVisto No 1 No Yes No No
FANMOD No 3 No Yes No No
tYNA Yes 0 No Yes No No
pajek Yes 2 No Yes Yes No
IsoRank No 0 No No No Yes
Graemlin No 0 No No No Yes
GraphM No 0 No No No Yes
  1. The "Graph Properties" column contains "Yes" if the package can compute at least the average diameter and clustering coefficient. The "# models" column corresponds to the number of random network model families supported by the package. The "Graphlets" column contains "Yes" if the package can count all graphlets and orbits in the network with up to 5 nodes and if it can compute signature similarities. The "Visualization" column contains "Yes" if the package is able to visualize graphs (graph drawing) or results (statistics). The "Clustering" and "GNA" Columns indicate whether the package supports clustering and Global Network Alignment (GNA), respectively.