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Nauty
A program for computing automorphism groups of graphs and digraphs. It can also produce a canonical labelling.
http://cs.anu.edu.au/~bdm/nauty/
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The LEDA Library
LEDA is a library of the data types and algorithms of combinatorial computing.
http://www.mpi-sb.mpg.de/LEDA/leda.html
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Free Software in Graph Theory
Free Software for Win 9X,NT on Graph Theory by Vitali Petchenkine. Procedures: Metrics of the graph; Paths and cycles; Colorations; Automorphism group; Minimal spanning tree; Shortest paths; Max. Capacity pa
http://www.geocities.com/pechv_ru/
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Gato: The Graph Animation Toolbox
Software for visualizing graph algorithms. Free under GPL. Unix, Linux, MacOs ad Windows versions.
http://www.zpr.uni-koeln.de/~gato
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plantri and fullgen
Programs for generation of certain types of planar graph, generated in such a way that exactly one member of each isomorphism class is output without the need for storing them.
http://cs.anu.edu.au/people/bdm/plantri/
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Algorithms and Software for Partitioning Meshes
Using combinatorics to solve structured linear systems of equations.
http://www.cs.sandia.gov/CRF/chac.html
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METIS: Family of Multilevel Partitioning Algorithms
Graph, mesh, and hypergraph partitioning software.
http://www-users.cs.umn.edu/~karypis/metis/
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SF, Posets and Coxeter/Weyl
John Stembridge's Maple packages for symmetric functions, posets, root systems, and finite Coxeter groups.
http://www.math.lsa.umich.edu/~jrs/maple.html
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Combinatorics Software of the Algorithms Project
Combinatorial analysis, discrete mathematics and computer algebra are the main interests of the Algorithms Projects. The packages let you define combinatorial structures; manipulate the associated generating functions, functional equations or recurrences
http://algo.inria.fr/libraries/software.html
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GraphThing
Tool for investigating Graph Theory, with a GTK interface. Free under GPL. Unix, source code in C++.
http://graph.seul.org/
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