RepeatScout is a tool to discover repetitive substrings in DNA.
The RepeatScout source code can be downloaded from the links bellow:
RepeatScout (new) release 1.0.3 , README
RepeatScout release 1.0.2 , README

If you use RepeatScout, please cite the following paper: 

Price A.L., Jones N.C. and Pevzner P.A. 2005.  De novo identification of 
repeat families in large genomes.  To appear in Proceedings of the
13 Annual International conference on Intelligent Systems for
Molecular Biology (ISMB-05).  Detroit, Michigan.

You may want to browse the ISMB PowerPoint presentation that explains the internals of the algorithm.

Available repeat libraries

The following libraries have been constructed by using version 1.0.0 of this software and filtering as described in the paper. Each of these is an uncompressed Fasta-formatted file, except for the last one, which is a compressed tape archive (that is, a "tarball").
This page maintained by Neil Jones. Last updated 6/19/2005.