DrawNet | ✓ | | | | | | | | | | | | | http://www.mrc-lmb.cam.ac.uk/genomes/rjanky/drawnet/ | – |

H3Viewer | ✓ | | | | | | | | | | | | | http://www-graphics.stanford.edu/~munzner/h3/ | [248] |

Graphviz | ✓ | ✓ | | | | | | | | | | | | http://www.graphviz.org/ | – |

Tulip | ✓ | ✓ | | | | | | | | | | | | http://tulip.labri.fr | [249] |

Biolayout | ✓ | ✓ | | | | | | | | | ✓ | | | http://www.biolayout.org/ | [250] |

Osprey | ✓ | ✓ | ✓ | | | | | | | | | | | http://biodata.mshri.on.ca/osprey | [251] |

Pajek | ✓ | ✓ | ✓ | ✓ | ✓ | | | | | | | | | http://vlado.fmf.uni-lj.si/pub/networks/pajek/ | [252] |

Yed | ✓ | ✓ | ✓ | ✓ | | | | | | | | | | http://www.yworks.com/ | – |

NetMiner | ✓ | ✓ | ✓ | ✓ | | ✓ | | | ✓ | | | | | http://www.netminer.com/ | – |

VANTED | ✓ | ✓ | ✓ | ✓ | | | ✓ | | | | ✓ | | | http://vanted.ipk-gatersleben.de/ | [253] |

VisANT | ✓ | ✓ | ✓ | ✓ | | | | ✓ | ✓ | ✓ | | | | http://visant.bu.edu/ | [254] |

Bioconductor | ✓ | ✓ | ✓ | ✓ | ✓ | | | | | | | | | http://www.bioconductor.org/ | [255] |

igraph | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | | ✓ | | ✓ | | | | http://igraph.sourceforge.net/ | – |

Cytoscape | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | | | http://www.cytoscape.org/ | [256] |

NeAT | ✓ | | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | | | http://rsat.scmbb.ulb.ac.be/neat/ | [257] |

TYNA/Topnet | ✓ | | ✓ | ✓ | | | ✓ | | | | | | | http://tyna.gersteinlab.org/tyna/ | [258] |

MCode | ✓ | | ✓ | ✓ | | | | ✓ | | | ✓ | | | http://baderlab.org/Software/MCODE | [259] |

NetMatch | ✓ | | | | ✓ | | | | | | | | | http://baderlab.org/Software/NetMatch | [260] |

MAVisto | ✓ | ✓ | | | ✓ | ✓ | | | | | | | | http://mavisto.ipk-gatersleben.de/ | [261] |

Mdraw | ✓ | | | | ✓ | ✓ | | | | | | | | http://www.weizmann.ac.il/mcb/ | – |

| | | | | | | | | | | | | | UriAlon/groupNetworkMotifSW.html | |

FanMod | | | | | ✓ | | | | | | | | | http://www.minet.uni-jena.de/~wernicke/motifs/ | [262] |

MFinder | | | | | ✓ | ✓ | | | | | | | | http://www.weizmann.ac.il/mcb/ | – |

| | | | | | | | | | | | | | UriAlon/groupNetworkMotifSW.html | |

CFinder | | | | | | | | | | ✓ | | | | http://www.cfinder.org/ | [263] |

Clique finder | | | | | | | | | | ✓ | | | | http://topnet.gersteinlab.org/clique/ | [264] |

BIOPROSPECTOR | | | | | | | | | | | | ✓ | | http://bioprospector.stanford.edu/ | [265] |

CISMODULE | | | | | | | | | | | | ✓ | | http://www.stat.ucla.edu/~zhou/CisModule/ | [266] |

EMCMODULE | | | | | | | | | | | | ✓ | | http://people.bu.edu/gupta/emcmodule.html | [267] |

GibbsModule | | | | | | | | | | | | ✓ | | http://biocomp.bioen.uiuc.edu/GibbsModule | [268] |

MEME | | | | | | | | | | | | ✓ | | http://meme.sdsc.edu/meme/ | [269] |

RSAT | | | | | | | | | | | | ✓ | ✓ | http://rsat.scmbb.ulb.ac.be/rsat/ | [270] |

seqVISTA | | | | | | | | | | | | ✓ | ✓ | http://zlab.bu.edu/SeqVISTA | [271] |

Virtual Footprint | | | | | | | | | | | | ✓ | ✓ | http://www.prodoric.de/vfp/ | [272] |

rVista | | | | | | | | | | | | ✓ | ✓ | http://rvista.dcode.org/ | [273] |

WebMOTIFS | | | | | | | | | | | | ✓ | ✓ | http://fraenkel.mit.edu/webmotifs | [274] |

PhyloNET | | | | | | | | | | | | | ✓ | http://bioinfo.cs.rice.edu/phylonet/index.html | [275] |

PROCSE | | | | | | | | | | | | | ✓ | http://www.biozentrum.unibas.ch/~nimwegen/cgi-bin/procse.cgi | [276] |

Regulogger | | | | | | | | | | | | | ✓ | http://regulogs.cgb.ki.se/REGULOGS | [277] |