Table 2 Description of computational programs to analyse networks

Adapted from [86].

ToolVisualizationDrawing/editingAnalysisNetwork topologyNetwork motifsRandomizationGraph comparisonSubnet-workNeighboursCliquesGraph clusteringMotif discoveryMotif clusteringWebsite (URL)Reference
DrawNethttp://www.mrc-lmb.cam.ac.uk/genomes/rjanky/drawnet/
H3Viewerhttp://www-graphics.stanford.edu/~munzner/h3/[248]
Graphvizhttp://www.graphviz.org/
Tuliphttp://tulip.labri.fr[249]
Biolayouthttp://www.biolayout.org/[250]
Ospreyhttp://biodata.mshri.on.ca/osprey[251]
Pajekhttp://vlado.fmf.uni-lj.si/pub/networks/pajek/[252]
Yedhttp://www.yworks.com/
NetMinerhttp://www.netminer.com/
VANTEDhttp://vanted.ipk-gatersleben.de/[253]
VisANThttp://visant.bu.edu/[254]
Bioconductorhttp://www.bioconductor.org/[255]
igraphhttp://igraph.sourceforge.net/
Cytoscapehttp://www.cytoscape.org/[256]
NeAThttp://rsat.scmbb.ulb.ac.be/neat/[257]
TYNA/Topnethttp://tyna.gersteinlab.org/tyna/[258]
MCodehttp://baderlab.org/Software/MCODE[259]
NetMatchhttp://baderlab.org/Software/NetMatch[260]
MAVistohttp://mavisto.ipk-gatersleben.de/[261]
Mdrawhttp://www.weizmann.ac.il/mcb/
UriAlon/groupNetworkMotifSW.html
FanModhttp://www.minet.uni-jena.de/~wernicke/motifs/[262]
MFinderhttp://www.weizmann.ac.il/mcb/
UriAlon/groupNetworkMotifSW.html
CFinderhttp://www.cfinder.org/[263]
Clique finderhttp://topnet.gersteinlab.org/clique/[264]
BIOPROSPECTORhttp://bioprospector.stanford.edu/[265]
CISMODULEhttp://www.stat.ucla.edu/~zhou/CisModule/[266]
EMCMODULEhttp://people.bu.edu/gupta/emcmodule.html[267]
GibbsModulehttp://biocomp.bioen.uiuc.edu/GibbsModule[268]
MEMEhttp://meme.sdsc.edu/meme/[269]
RSAThttp://rsat.scmbb.ulb.ac.be/rsat/[270]
seqVISTAhttp://zlab.bu.edu/SeqVISTA[271]
Virtual Footprinthttp://www.prodoric.de/vfp/[272]
rVistahttp://rvista.dcode.org/[273]
WebMOTIFShttp://fraenkel.mit.edu/webmotifs[274]
PhyloNEThttp://bioinfo.cs.rice.edu/phylonet/index.html[275]
PROCSEhttp://www.biozentrum.unibas.ch/~nimwegen/cgi-bin/procse.cgi[276]
Reguloggerhttp://regulogs.cgb.ki.se/REGULOGS[277]