- 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 TRF version 4.0.4
- Repeat Database
RepeatMasker will now work with custom libraries, Dfam, and with Dfam_consensus
out of the box. Dfam is a database of Transposable Element profile HMM models.
The current release ( Dfam2.0 ) contains 4,150 models
spanning five organisms: human, mouse, zebrafish, fruit fly,
and nematode. Dfam_consensus is a new open database of Transposable Element consensus
sequences. To supplement these growing databases we highly recommend
obtaining the RepeatMasker edition of RepBase. RepeatMasker
searches are optimised to use these databases 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 RepeatMasker Edition go to
To obtain updated Dfam_consensus and RepeatMasker metadata click
- Download RepeatMasker
Latest Released Version: 2/1/2017: RepeatMasker-open-4-0-7.tar.gz
Previous Released Version: 10/29/2015: RepeatMasker-open-4-0-6.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/ ). Make sure you do not extract in a directory already containing a pre-existing directory called "RepeatMasker" as it will attempt to overwrite files contained within.
- 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
RepeatMasker now comes with two small, but growing open databases ( Dfam and Dfam_consensus ) and will work out-of-the box with these datasets. However it is advised that you also obtain a license for the RepBase RepeatMasker Edition to supplement these sequences. To obtain a license and download the library go to http://www.girinst.org.
Once you have obtain the library ( current version is RepBaseRepeatMaskerEdition-20170127.tar.gz ) file from GIRI unpack it in the RepeatMasker directory and it will automatically place the contents in the correct subdirectories.
- cp RepBaseRepeatMaskerEdition-########.tar.gz /usr/local/RepeatMasker/
- cd /usr/local/RepeatMasker
- gunzip RepBaseRepeatMaskerEdition-########.tar.gz
- tar xvf RepBaseRepeatMaskerEdition-########.tar
- rm RepBaseRepeatMaskerEdition-########.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. The RepeatMasker distribution contains the Dfam 2.0 library.
- Run Configure Script
The program requires some initial configuration. This should also be re-run after future updates to the library files.
- 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-3.0/4.0" is licensed under the Open Source License v2.1.
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