1. Unix system with perl 5.8.0 or higher installed
2. Sequence Search Engine
   RepeatMasker uses a sequence search engine to perform it's search for repeats. Currently Cross_Match, RMBlast and WUBlast/ABBlast are supported. You will need to obtain one or the other of these and install them on your system.
   • For Cross_Match go to http://www.phrap.org You will want to select "Phred/Phrap/Consed" as Cross_Match is part of the Phrap package.
   • For RMBlast ( NCBI Blast modified for use with RepeatMasker/RepeatModeler ) please go to our download page: http://www.repeatmasker.org/RMBlast.html
   • For HMMER please download the prerelease version here: ftp://selab.janelia.org/pub/pickup/hmmer3.1-snap20121016.1.tgz
   • For ABBlast/WUBlast go to [ NOTE: Rights to BLAST 2.0 (WU-BLAST) have been acquired by Advanced Biocomputing, LLC. http://blast.advbiocomp.com/licensing/ RepeatMasker 3.2.8 and above fully support both variants ]
3. TRF - Tandem Repeat Finder, G. Benson et al.
   You can obtain a free copy at http://tandem.bu.edu/trf/trf.html. RepeatMasker was developed using 4.0.4
4. Repeat Database
   RepeatMasker will now work with custom libraries and with Dfam out of the box. Dfam is a database of profile HMM models of transposable elements ( only human at this point ) and is supported by RepeatMasker. For all other species we highly recommend obtaining the RepeatMasker version of RepBase. RepeatMasker searches are optimised to use this database and can produce higher quality annotations than can be acheived using the equivalent libraries with the -lib option.
   To update the Dfam libraries contained in this release go to http://www.dfam.org.
   To obtain RepBase for RepeatMasker go to http://www.girinst.org.

1. Download RepeatMasker
   Latest Released Version: 4/29/2013: RepeatMasker-open-4-0-2.tar.gz
   Previous Released Version: 6/22/2012: RepeatMasker-open-3-3-0-p1.tar.gz
   
2. Unpack Distribution
   Unpack the distribution in your home directory or in a location where it may be shared with other users of your system ( ie. /usr/local/ ).
   • cp RepeatMasker-open-4-#-#.tar.gz /usr/local
   • cd /usr/local
   • gunzip RepeatMasker-open-4-#-#.tar.gz
   • tar xvf RepeatMasker-open-4-#-#.tar
3. Install RepeatMasker Libraries
   Download the libraries from http://www.girinst.org and unpack in the RepeatMasker program directory. This version supports the following libraries ( it is always best to use the most current ): repeatmaskerlibraries-20130422.tar.gz and later.
   • cp repeatmaskerlibraries-########.tar.gz /usr/local/RepeatMasker/
   • cd /usr/local/RepeatMasker
   • gunzip repeatmaskerlibraries-########.tar.gz
   • tar xvf repeatmaskerlibraries-########.tar
   • rm repeatmaskerlibraries-########.tar
4. Check for Dfam Updates ( optional )
   Download the Dfam.hmm.gz library from http://www.dfam.org and save it to the RepeatMasker/Libraries directory. Uncompress the file before using RepeatMasker.
5. Run Configure Script
   The program requires some configuration before use. There is now a script which assists in making these changes.
   • cd /usr/local/RepeatMasker
   • perl ./configure
6. Subscribe to announcements list
   The rmannounce mailing list is an important way to hear about bugs and new releases. This is a one-way list ( posting is not allowed ). The traffic from the list is low and generally mimics the major announcements shown on the main website. To subscribe fill in the form at the bottom of this page.

RepeatMasker "open-3.0" is licensed under the Open Source License v2.1.