- Unix system with perl 5.8.0 or higher installed
- 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
- TRF - Tandem Repeat Finder, G. Benson et al.
You can obtain a free copy at
RepeatMasker was developed using 4.0.4
- 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
To obtain RepBase for RepeatMasker go to
- 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
- 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
- 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
- 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.
- 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
- 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.
Subscribing to the rmannounce Mailing List
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