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

BMC Bioinformatics

Table 2 Comparison of software tools for biological network analysis

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

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.