- 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 and has been tested with 4.0.9
- 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
- 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.
- 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 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 http://www.girinst.org.
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
- 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 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.
Input files containing multiple FASTA sequences
caused RepeatMasker to error out with a message
"WARNING: TRF returned an error (Return code = ### )
TRF parameters: 184.108.40.206.10.50.10
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.