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This package contains the source code accompanying the paper Falk Hüffner, Sebastian Wernicke, and Thomas Zichner: Algorithm engineering for color-coding with applications to signaling pathway detection. Algorithmica, 52(2):114–132, 2008. http://dx.doi.org/10.1007/s00453-007-9008-7 http://falk.hueffner.de/color-coding-algorithmica07.pdf A slightly updated description is in the thesis Falk Hüffner: Algorithms and Experiments for Parameterized Approaches to Hard Graph Problems. PhD thesis, Institut für Informatik, Friedrich-Schiller-Universität Jena, 2007. http://hueffner.de/falk/diss-hueffner07.pdf Command line program ==================== It can solve two problems (see paper): * Find minimum-weight paths of a prespecified length in a weighted undirected graph. * Path queries. The program is written in ISO C++. It has only been tested on Unix systems, but should be portable to other systems. Sources can be obtained at http://theinf1.informatik.uni-jena.de/colorcoding/. They are distributed under the terms of the GNU General Public License (GPL, see COPYING). It has been tested on: * Debian GNU/Linux (x86-64) with GNU g++ 4.3.5 and 4.4.5 Previous versions have been tested on: * Debian GNU/Linux (i386) 3.1 with GNU g++ 3.3.5, 3.4.4, and 4.1.0 * Digital Unix 5.1 (Alpha) with GNU g++ 3.3.2 and DEC C++ V6.3-008 (needs the "-std strict_ansi" option) * Solaris 9 (UltraSPARC) with GNU g++ 4.0.2 * Windows XP/Cygwin 1.4 If you have the "make" utility (as any Unix system has), you can compile with "make". The program is called "colorcoding". By default, it reads a graph from standard input and writes the paths found to standard output. The graph format is a simple text format, where each line describes one edge, given by its two endpoints and the edge weight separated by whitespace: v0 v1 0.32 v1 v2 1.22 v2 v0 0.01 Vertex names can be any combination of letters, digits, and _. Note that this graph format cannot describe degree-0 vertices; however, they are irrelevant for finding paths anyway. The output is a set of (by default 100) paths of minimum weight in the graph. Each line describes one path by giving its total weight and the list of vertices. Example: # ./colorcoding < example.graph 1.73 10 3 5 4 7 2 1 6 There are many options that affect program behavior; see ./colorcoding -h for a listing. Version history --------------- 1.0 2006-05-10 initial release 1.1 2006-11-01 path query functionality added 1.1.1 2008-10-26 missing files added to .tar.gz 1.1.2 2010-08-13 add -w option add -L option fix some minor bugs -- Falk Hüffner (http://hueffner.de/falk/)
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