RepeatFinder: finding 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 RepeatFinder
depends on Stefan Kurtz's REPuter.  Enjoy!

System requirements

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.

Obtaining RepeatFinder

This software is  OSI Certified Open Source Software .

To download RepeatFinder, just click here .

To download ClosureRepeatFinder, just click here.

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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