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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

Groups and Graphs
A software package for graphs, digraphs, combinatorial designs, and their automorphism groups.
http://130.179.24.217/G&G/G&G.html

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.
http://www.geocities.com/pechv_ru/

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.
http://www.npac.syr.edu/NPAC1/PUB/ranka/part/part.html

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

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/

GRAPE
A GAP share-package for computing with graphs; primarily designed for the efficient construction and analysis of graphs related to groups, combinatorial designs and finite geometries.
http://www.gap-system.org/Share/grape.html

Algorithms and Software for Partitioning Meshes
Using combinatorics to solve structured linear systems of equations.
http://www.cs.sandia.gov/CRF/chac.html

METIS: Family of Multilevel Partitioning Algorithms
Graph, mesh, and hypergraph partitioning software.
http://www-users.cs.umn.edu/~karypis/metis/

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

Graph Partitioners
Three algorithms written in NESL for finding separators of graphs, in order to compare the quality of the cuts.
http://www.cs.cmu.edu/~scandal/alg/separator.html

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.
http://algo.inria.fr/libraries/software.html

GraphThing
Tool for investigating Graph Theory, with a GTK interface. Free under GPL. Unix, source code in C++.
http://graph.seul.org/

ACE
An Algebraic Combinatorics Environment for MAPLE providing functions to work with classical structures in algebraic combinatorics. Free download.
http://phalanstere.univ-mlv.fr/~ace/

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.
http://dimacs.rutgers.edu/~berryj/LINK.html

Graph Coloring By DSATUR
By using the DSATUR algorithm, this php/form colors any graph in the Dimacs format.
http://prolland.free.fr/works/research/dsatphp/dsat.html

Project Vega
A system for manipulating discrete mathematical structures: a Mathematica based collection of operations with interface to external packages and programs.
http://vega.ijp.si/

JGraphT
Free Java class library that provides mathematical graph-theory objects and algorithms.
http://jgrapht.sourceforge.net

GeoSteiner
Software for computing Steiner trees. Written in ANSI C, includes the public domain LP-solver lp_solve.
http://www.diku.dk/geosteiner/

Formula
Software for gambling, probability and statistical calculations: standard deviation, binomial distribution, Gauss curve, normal distribution, odds, median, mean, average, sum.
http://www.saliu.com/formula.html

Information System on Graph Class Inclusions
A java applet for researching what is known about particular graph classes.
http://wwwteo.informatik.uni-rostock.de/isgci/

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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