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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.
http://www.maths.qmul.ac.uk/~leonard/grape/
Qmul.ac.uk ~
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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/ACE/3.0/ACE.html
Univ-mlv.fr ~
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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.
http://www.graph-magics.com
Graph-magics.com ~
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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.
http://graph-utils.sourceforge.net
Sourceforge.net ~
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