Nauty - A program for computing automorphism groups of graphs and digraphs. It can also produce a canonical labelling.
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.
Scalable Libraries for Graph Partitioning - We are pursuing research in the area of new parallel methods for graph partitioning and incremental graph partitioning. Efficient methods for graph partitioning and incremental graph partitioning are important for parallelization of a large number of unstructured and/or adaptive applications.
Gato: The Graph Animation Toolbox - Software for visualizing graph algorithms. Free under GPL. Unix, Linux, MacOs ad Windows versions.
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.
Algorithms and Software for Partitioning Meshes - Using combinatorics to solve structured linear systems of equations.
METIS: Family of Multilevel Partitioning Algorithms - Graph, mesh, and hypergraph partitioning software.
SF, Posets and Coxeter/Weyl - John Stembridge's Maple packages for symmetric functions, posets, root systems, and finite Coxeter groups.
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.
GraphThing - Tool for investigating Graph Theory, with a GTK interface. Free under GPL. Unix, source code in C++.
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.
Graph Coloring By DSATUR - By using the DSATUR algorithm, this php/form colors any graph in the Dimacs format.
JGraphT - Free Java class library that provides mathematical graph-theory objects and algorithms.
GeoSteiner - Software for computing Steiner trees. Written in ANSI C, includes the public domain LP-solver lp_solve.
Information System on Graph Class Inclusions - A java applet for researching what is known about particular graph classes.
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.
GOBLIN Graph Library - C++ library of graph optimization algorithms with a GUI for editing, running and tracing the algorithms.
ACE - An Algebraic Combinatorics Environment for MAPLE providing functions to work with classical structures in algebraic combinatorics. Free download.
Project Vega - A system for manipulating discrete mathematical structures: a Mathematica based collection of operations with interface to external packages and programs.
NetworkX - NetworkX (NX) is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
Graph Magics - A tool for graph theory, having a generator and offering various algorithms: shortest paths, network flows, maximal clique, optimal coloring etc.
Graph Partitioners - Three algorithms written in NESL for finding separators of graphs, in order to compare the quality of the cuts.
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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