- Unix system with perl 5.8.0 or higher installed
- Python 3 and the h5py python library.
- 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 4.0.9
- 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
- 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
- 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 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
- 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.
- 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
- 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.
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 now has a refactored configuration system
making it easier to distribute RepeatMasker via package
managers and/or bundle RepeatMasker into containers.
Input files containing multiple FASTA sequences
caused RepeatMasker to error out with a message
"WARNING: TRF returned an error (Return code = ### )
TRF parameters: 18.104.22.168.10.50.10
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
- 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.