The Institute for Systems Biology RepeatMasker Download

  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.
  3. TRF - Tandem Repeat Finder, G. Benson et al.
    You can obtain a free copy at RepeatMasker was developed using TRF version 4.0.4
  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 here.
  1. Download RepeatMasker
    Latest Released Version: 11/21/2018: RepeatMasker-open-4-0-8.tar.gz
    Previous Released Version: 2/1/2017: RepeatMasker-open-4-0-7.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/ ). 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
  3. 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 Once you have obtain the library ( current version is RepBaseRepeatMaskerEdition-20181026.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
  4. Check for Dfam Updates ( optional )
    Download the Dfam.hmm.gz library from and save it to the RepeatMasker/Libraries directory. Uncompress the file before using RepeatMasker. The RepeatMasker distribution contains the Dfam 2.0 library.
  5. 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

RepeatMasker "open-3.0/4.0" is licensed under the Open Source License v2.1.

Institute for Systems Biology
This server is made possible by funding from the National Human Genome Research Institute (NIGRI grant # RO1 HG002939).