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GAP
GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. GAP provides a programming language, a library of thousands of functions implementing algebraic algorithms written in the GAP language as well as large data libraries of algebraic objects. GAP is used in research and teaching for studying groups and their representations, rings, vector spaces, algebras, combinatorial structures, and more. GAP is developed by international cooperation. The system, including source, is distributed freely under the terms of the GNU General Public License. You can study and easily modify or extend GAP for your special use. The current version is GAP 4, the older version GAP 3 is still available.
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igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is a free and open source software package for creating and manipulating undirected and directed graphs. It includes implementations for classic graph theory problems like minimum spanning trees and network flow, and also implements algorithms for some recent network analysis methods, like community structure search. The efficient implementation of igraph allows it to handle graphs with millions of vertices and edges. The rule of thumb is that if your graph fits into the physical memory then igraph can handle it. igraph can be programmed in R, Python and C/C++ by virtue of R/igraph, python-igraph and C/igraph, respectively. There is also a Mathematica interface IGraph/M written by Szabolcs Horvát.
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Nauty is a program for computing automorphism groups of graphs and digraphs. It can also produce a canonical labelling.
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