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Graph-tool
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<h2 id="features">Features</h2> <ul><li>Creation and manipulation of <a href="/facts/Directed_graph/YBdfQ0um">directed</a> or <a href="/facts/Graph_(discrete_mathematics)/kw3eIBUe">undirected graphs</a>.</li> <li>Association of arbitrary information to the vertices, edges or even the graph itself, by means of property maps.</li> <li>Filter vertices and/or edges "on the fly", such that they appear to have been removed.</li> <li>Support for <a href="/facts/DOT_language/RbNL4cRd">dot</a>, <a href="/facts/Graph_Modelling_Language/xUHP500h">Graph Modelling Language</a> and <a href="/facts/GraphML/myvj1vav">GraphML</a> formats.</li> <li>Convenient and powerful <a href="/facts/Graph_drawing/uhh73BVo">graph drawing</a> based on <a href="/facts/Cairo_(graphics)/FuAWHozI">cairo</a> or <a href="/facts/Graphviz/nf5D4paX">Graphviz</a>.</li> <li>Support for typical statistical measurements: degree/property histogram, combined degree/property histogram, vertex-vertex correlations, <a href="/facts/Assortativity/vPa7v9Pz">assortativity</a>, average vertex-vertex <a href="/facts/Shortest_path/g4nsrswr">shortest path</a>, etc.</li> <li>Support for several graph-theoretical algorithms: such as <a href="/facts/Graph_isomorphism/SBjVIhwW">graph isomorphism</a>, <a href="/facts/Subgraph_isomorphism_problem/86LLWRg4">subgraph isomorphism</a>, <a href="/facts/Minimum_spanning_tree/kgkGmY9s">minimum spanning tree</a>, <a href="/facts/Connected_component_(graph_theory)/5owVSXtY">connected components</a>, <a href="/facts/Dominator_(graph_theory)/PILJwzWc">dominator</a> tree, <a href="/facts/Maximum_flow/aSal0FGF">maximum flow</a>, etc.</li> <li>Support for several <a href="/facts/Centrality/4n24KqLt">centrality</a> measures.</li> <li>Support for <a href="/facts/Clustering_coefficient/yB6Q3gk2">clustering coefficients</a>, as well as <a href="/facts/Network_motif/osqmLDSy">network motif</a> statistics and <a href="/facts/Community_structure/CKfUKFYh">community structure</a> detection.</li> <li>Generation of <a href="/facts/Random_graphs/gfQhq1Sz">random graphs</a>, with arbitrary degree distribution and correlations.</li> <li>Support for well-established network models: <a href="/facts/Preferential_attachment/9u0eN8nd">Price</a>, <a href="/facts/Barab%C3%A1si%E2%80%93Albert_model/lNqLTRsP">Barabási-Albert</a>, Geometric Networks, Multidimensional <a href="/facts/Lattice_graph/4EHMt1b6">lattice graph</a>, etc.</li></ul> <h2 id="suitability">Suitability</h2> <p>Graph-tool can be used to work with very large graphs in a variety of contexts, including simulation of <a href="/facts/Epithelium/ecKHcHC3">cellular tissue</a>,<a class="footnote-ref" id="fnref:2" href="#fn:2"><sup>2</sup></a> <a href="/facts/Data_mining/AH53q5ac">data mining</a>,<a class="footnote-ref" id="fnref:3" href="#fn:3"><sup>3</sup></a><a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a> <a href="/facts/Social_network_analysis/CsJIFjVw">analysis of social networks</a>,<a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a><a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> analysis of <a href="/facts/Peer-to-peer/wCCdPb0H">P2P</a> systems,<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> large-scale modeling of <a href="/facts/Agent-based_model/C3C1vR8s">agent-based systems</a>,<a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a> study of academic <a href="/facts/Genealogy_tree/KxTrDYQA">Genealogy trees</a>,<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> theoretical assessment and modeling of network <a href="/facts/Clustering_coefficient/yB6Q3gk2">clustering</a>,<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a> large-scale <a href="/facts/Call_graph/Uk0b0mdN">call graph</a> analysis,<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a> and analysis of the brain's <a href="/facts/Connectome/X5tjEwwl">Connectome</a>.<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a> </p> <h2 id="external-links">External links</h2> <ul> <li>Free and open-source software portal</li></ul> <ul><li><a href="http://graph-tool.skewed.de">Official website</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Graph-tool performance comparison, Graph-tool <a href="http://graph-tool.skewed.de/performance" target="_blank">http://graph-tool.skewed.de/performance</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Bruno Monier et al, "Apico-basal forces exerted by apoptotic cells drive epithelium folding", Nature, 2015 [1] <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14152.html" target="_blank">http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14152.html</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Ma, Shuai, et al. "Distributed graph pattern matching." Proceedings of the 21st international conference on World Wide Web. ACM, 2012. [2] <a href="http://dl.acm.org/citation.cfm?id=2187963" target="_blank">http://dl.acm.org/citation.cfm?id=2187963</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Ma, Shuai, et al. "Capturing topology in graph pattern matching." Proceedings of the VLDB Endowment 5.4 (2011): 310-321. [3] <a href="http://dl.acm.org/citation.cfm?id=2095690" target="_blank">http://dl.acm.org/citation.cfm?id=2095690</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Janssen, E., M. A. T. T. Hurshman, and N. A. U. Z. E. R. Kalyaniwalla. "Model selection for social networks using graphlets." Internet Mathematics (2012). [4] <a href="http://www.mathstat.dal.ca/~janssen/papers/Graphlets.pdf" target="_blank">http://www.mathstat.dal.ca/~janssen/papers/Graphlets.pdf</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Asadi, Hirad Cyrus. Design and implementation of a middleware for data analysis of social networks. Diss. M Sc thesis report, KTH School of Computer Science and Communication, Stockholm, Sweden, 2007. [5] Archived 2015-01-22 at the Wayback Machine <a href="http://www.student.nada.kth.se/~hias02/xjobb-en.pdf" target="_blank">http://www.student.nada.kth.se/~hias02/xjobb-en.pdf</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Teresniak, Sven, et al. "Information-Retrieval in einem P2P-Netz mit Small-World-Eigenschaften Simulation und Evaluation des SemPIR-Modells."[6] Archived 2015-01-22 at the Wayback Machine <a href="http://asv.informatik.uni-leipzig.de/thesis/thesis_document/25/masterarbeit.pdf" target="_blank">http://asv.informatik.uni-leipzig.de/thesis/thesis_document/25/masterarbeit.pdf</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Hamacher, Kay, and Stefan Katzenbeisser. "Public security: simulations need to replace conventional wisdom." Proceedings of the 2011 workshop on New security paradigms workshop. ACM, 2011. [7] <a href="http://dl.acm.org/citation.cfm?id=2073288" target="_blank">http://dl.acm.org/citation.cfm?id=2073288</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Miyahara, Edson Kiyohiro, Jesus P. Mena-Chalco, and Roberto M. Cesar-Jr. "Genealogia Acadêmica Lattes." [8][permanent dead link] <a href="http://www.linux.ime.usp.br/~edsonkm/mac499/download/monografia.pdf" target="_blank">http://www.linux.ime.usp.br/~edsonkm/mac499/download/monografia.pdf</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Abdo, Alexandre H., and A. P. S. de Moura. "Clustering as a measure of the local topology of networks." arXiv preprint physics/0605235 (2006). [9] <a href="https://arxiv.org/abs/physics/0605235" target="_blank">https://arxiv.org/abs/physics/0605235</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Narayan, Ganesh, K. Gopinath, and V. Sridhar. "Structure and interpretation of computer programs." Theoretical Aspects of Software Engineering, 2008. TASE'08. 2nd IFIP/IEEE International Symposium on. IEEE, 2008. [10] <a href="https://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4549888" target="_blank">https://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4549888</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Gerhard, Stephan, et al. "The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes." Frontiers in neuroinformatics 5 (2011). [11] <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112315/" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112315/</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> </ol>