repetitive sequences complete and draft genomes
This directory contains two programs for
finding repeats in genomic DNA sequences. The first program,
described in the paper by Volfovsky et al. (2001) Genome Biology is
RepeatFinder. Get the reprint
here. A second program, designed specifically to find
repeats likely to confuse a genome assembly, is called
ClosureRepeatFinder. The two programs are quite different and
have different purposes; RepeatFinder is intended to be the more
comprehensive approach. Both are open source; note that
depends on Stefan Kurtz's REPuter. Enjoy!
Both programs are released as source code and were tested on
Linux RedHat 6.x+, Sun Solaris, and Alpha OSF1, but should work on any
Unix system. These have been run on newer Linux versions as well,
but we are not supporting upgrades at present.
This software is OSI Certified
Open Source Software .
To download RepeatFinder, just click
To download ClosureRepeatFinder, just click
After downloading, uncompress the distribution file by typing:
% tar -xzf RepeatFinder.tar.gz
The project was supported in part by NIH
Award R01-LM06845 to S.L. Salzberg
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