| |
Software
Addibit is Another Double Description Implementation with BInary Trees. It uses bit pattern [1,2] and vantage point trees [3]. This is only a repository snapshot which may (and surely does) contain a lot of bugs.
Check the README-file for instructions of how to compile and run the program. For an overview of the double description method check [4].
Here is a small study comparing the performance of the different trees types supported by addibit.
|
[1]
|
M. Terzer and J. Stelling.
Accelerating the computation of elementary modes using pattern trees.
In Proceedings of the 6th international conference on Algorithms
in Bioinformatics, WABI '06, pages 333-343, Berlin/Heidelberg, 2006.
Springer-Verlag.
[ bib ]
|
|
[2]
|
M. Terzer and J. Stelling.
Large-scale computation of elementary flux modes with bit pattern
trees.
Bioinformatics, 24:2229-2235, 2008.
[ bib ]
|
|
[3]
|
Peter N. Yianilos.
Data structures and algorithms for nearest neighbor search in general
metric spaces.
In Proceedings of the fourth annual ACM-SIAM Symposium on
Discrete algorithms, SODA '93, pages 311-321, Philadelphia, PA, USA, 1993.
Society for Industrial and Applied Mathematics.
[ bib ]
|
|
[4]
|
K. Fukuda and A. Prodon.
Double description method revisited.
In Combinatorics and Computer Science, volume 1120 of
Lecture Notes in Computer Science, pages 91-111. Springer-Verlag,
Berlin/Heidelberg, 1996.
[ bib ]
|
Dipl.-Inf. Blagoy Genov
E-mail: bgenov@informatik.uni-bremen.de
|
|
FB3