The Institute for Systems Biology RepeatMasker Download

Prerequisites
  1. Unix system with perl 5.8.0 or higher installed
  2. Python 3 and the h5py python library.
  3. 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.
  4. 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 TRF version 4.0.9
  5. Repeat Database
    RepeatMasker can be used with custom libraries, or 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 3.2) contains 6,900 TE families spanning five organisms: human, mouse, zebrafish, fruit fly, nematode, and a growing number of additional species. To supplement this databases we recommend obtaining the RepeatMasker edition of RepBase.
    To update the Dfam libraries contained in this release go to http://www.dfam.org.
Installation
  1. Download RepeatMasker
    Latest Released Version: 09/03/20: RepeatMasker-4.1.1.tar.gz
    Previous Released Version: 10/30/19: RepeatMasker-4.1.0.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 comes with a copy of the curated portion of Dfam ( Libraries/Dfam.h5 ) and will work out-of-the box with this library. This is a small library ( at this time ). There are two options for supplementing the main RepeatMasker library:
    • The complete Dfam ( curated and uncurated families ) library may be downloaded from www.dfam.org in famdb HDF5 format and used to replace the distributed "Libraries/dfam.h5" file. For example:
      • wget https://www.dfam.org/releases/Dfam_3.2/families/Dfam.h5.gz
      • gunzip Dfam.h5.gz
      • mv Dfam.h5 /usr/local/RepeatMasker/Libraries
        • NOTE: This will overwrite the distributed Dfam.h5 file.
    • and/or:
    • The RepBase RepeatMasker Edition ( final version 10/26/2018 ) may be downloaded from www.girinst.org and unpaked in the RepeatMasker directory. For example:
      • cp RepBaseRepeatMaskerEdition-20181026.tar.gz /usr/local/RepeatMasker/
      • cd /usr/local/RepeatMasker
      • gunzip RepBaseRepeatMaskerEdition-20181026.tar.gz
      • tar xvf RepBaseRepeatMaskerEdition-20181026.tar
      • rm RepBaseRepeatMaskerEdition-20181026.tar
  4. 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
RepeatMasker-4.1.1

  • Dfam (starting with version 3.2) is now distributed in the FamDB file format based on HDF5, which has improved support for large datasets compared to the EMBL and HMM formats that were previously used. RepeatMasker therefore includes a copy of famdb.py, and depends on the python package h5py.
    • The 'configure' script and other parts of RepeatMasker have been updated to accomodate these changes.
    • The utilities 'queryTaxonomyDatabase.pl' and 'queryRepeatDatabase.pl' are no longer included, since that data is now included in FamDB. The 'famdb.py' tool can be used to make many of the same queries as the removed utilies, and even more.
RepeatMasker-4.1.0

  • RepeatMasker now has a refactored configuration system making it easier to distribute RepeatMasker via package managers and/or bundle RepeatMasker into containers.
RepeatMasker-open-4-0-9-p1

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

    "WARNING: TRF returned an error (Return code = ### )
    TRF parameters: 2.7.7.80.10.50.10
    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.

RepeatMasker-open-4-0-9

  • 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.
Archived Releases

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