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 and has been tested with 4.0.9
  4. Repeat Database
    RepeatMasker will now work with custom libraries, and with Dfam out of the box. Dfam is an open database of transposable element (TE) profile HMM models and consensus sequences. The current release (Dfam 3.0) contains 6,235 TE families spanning five organisms: human, mouse, zebrafish, fruit fly, nematode, and a growing number of additional species. To supplement this 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
  1. Download RepeatMasker
    Latest Released Version: 4/9/19 (5/6/19 p2): RepeatMasker-open-4-0-9-p2.tar.gz

    Patch 1: Fixed a problem with the intrepretation of TRF return codes for files containing multiple FASTA sequences.
    Patch 2: Fixed another TRF issue related to changes between TRF4.0.8 and TRF4.0.9.

    Previous Released Version: 11/21/2018 (patched 4/5/19): RepeatMasker-open-4-0-8.tar.gz

    NOTE: Users reported that the original release file for 4.0.8 was incorrectly built. It was missing Dfam 2.0 (Libraries/Dfam.hmm) and the version was reporting as "RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $". Because there was no other functional change we have fixed the release file here and at the GitHub release site for 4.0.8. You do not need to re-download this version unless you need the program label to be correct.

  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 the open Dfam database and will work out-of-the box with this library. 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 obtaianed 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. Then complete the installation by running ( or rerunning ) the configure program to prepare the libraries for RepeatMasker use.
    • 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 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.

Release Notes

  • Input files containing multiple FASTA sequences caused RepeatMasker to error out with a message like:

    "WARNING: TRF returned an error (Return code = ### )
    TRF parameters:
    A search phase could not complete on this batch.
    The batch file will be re-run and if possible the
    program will resume.
    WARNING: Retrying batch ( 1 ) [ 255,, 195]..."

    This bug was introduced when we attempted to improve TRF error catching. Unfortunatly the return codes are not documented for TRF and the assumption that 256 is the only successful return code is wrong. The "success" code appears to change depending on the number of sequences in the file. The workaround is to fail only if there is a message in the error output file.


  • General compatibility update for Dfam 3.0. Dfam and Dfam_consensus have merged into one combined database. RepeatMasker can use Dfam using any of it search engines and will automatically switch to using consensus sequences or profile HMMs based on the engine used. It is important to note that, by default RepeatMasker will use Dfam consensus sequences when library duplicates are detected.
  • Bugfix: The -dir option no longer assumes that the directory already exists.
  • Feature: The configure script now accepts command-line parameters to change configuration settings. Configure also re-reads existing configuration options to use as prompt defaults.

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