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Nauty (Popularity:  ): A program for computing automorphism groups of graphs and digraphs. It can also produce a canonical labelling.
The LEDA Library (Popularity: ): LEDA is a library of the data types and algorithms of combinatorial computing.
plantri and fullgen (Popularity: ): 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.
METIS: Family of Multilevel Partitioning Algorithms (Popularity: ): Graph, mesh, and hypergraph partitioning software.
SF, Posets and Coxeter/Weyl (Popularity: ): John Stembridge's Maple packages for symmetric functions, posets, root systems, and finite Coxeter groups.
Combinatorics Software of the Algorithms Project (Popularity: ): 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 ...
GraphThing (Popularity: ): Tool for investigating Graph Theory, with a GTK interface. Free under GPL. Unix, source code in C++.
LINK: A Software System for Discrete Mathematics (Popularity: ): A general-purpose, extendible computing environment in which discrete mathematical objects representing real world problems can be easily manipulated and visualized.
Graph Coloring By DSATUR (Popularity: ): By using the DSATUR algorithm, this php/form colors any graph in the Dimacs format.
JGraphT (Popularity: ): Free Java class library that provides mathematical graph-theory objects and algorithms.
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