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The LEDA Library 
- LEDA is a library of the data types and algorithms of combinatorial computing.
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ACE - An Algebraic Combinatorics Environment for MAPLE providing functions to work with classical structures in algebraic combinatorics. Free download.
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Algorithms and Software for Partitioning Meshes - Using combinatorics to solve structured linear systems of equations.
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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; study their asymptotic behaviour.
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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 path; K Shortest paths; Salesman problem; Maximal flow; Critical path; Reports for Graphs; Print.
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Gato: The Graph Animation Toolbox - Software for visualizing graph algorithms. Free under GPL. Unix, Linux, MacOs ad Windows versions.
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GeoSteiner - Software for computing Steiner trees. Written in ANSI C, includes the public domain LP-solver lp_solve.
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GOBLIN Graph Library - C++ library of graph optimization algorithms with a GUI for editing, running and tracing the algorithms.
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GRAPE - A GAP package for computing with graphs; primarily designed for the efficient construction and analysis of graphs related to groups, combinatorial designs and finite geometries.
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Graph Coloring By DSATUR - By using the DSATUR algorithm, this php/form colors any graph in the Dimacs format.
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Graph Magics - A tool for graph theory, having a generator and offering various algorithms: shortest paths, network flows, maximal clique, optimal coloring etc.
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Graph Partitioners - Three algorithms written in NESL for finding separators of graphs, in order to compare the quality of the cuts.
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GraphThing - Tool for investigating Graph Theory, with a GTK interface. Free under GPL. Unix, source code in C++.
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graph-utils - A set of small utilities realizing theoretical graph algorithms (including tree algorithms). The utilities work with simple text input/output formats.
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Information System on Graph Class Inclusions - A java applet for researching what is known about particular graph classes.
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JGraphT - Free Java class library that provides mathematical graph-theory objects and algorithms.
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LINK: A Software System for Discrete Mathematics - A general-purpose, extendible computing environment in which discrete mathematical objects representing real world problems can be easily manipulated and visualized.
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METIS: Family of Multilevel Partitioning Algorithms - Graph, mesh, and hypergraph partitioning software.
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Nauty - A program for computing automorphism groups of graphs and digraphs. It can also produce a canonical labelling.
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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.
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SCL - star complement library - A program for calculating the maximal graphs using the star complement technique. The programs for computing the maximal cliques and isomorphism classes of graphs are included.
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