- 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
- For Cross_Match go to
You will want to select "Phred/Phrap/Consed" as
Cross_Match is part of the Phrap package.
- For RMBlast ( NCBI Blast modified for use with RepeatMasker/RepeatModeler ) please go to our download page: http://www.repeatmasker.org/RMBlast.html. It is highly recommended to use 2.13.0 or higher.
- For HMMER please download the v3.2.1 version here: http://hmmer.org/
- For ABBlast/WUBlast go to [ NOTE: Rights to BLAST 2.0 (WU-BLAST) have been acquired by Advanced Biocomputing, LLC. http://blast.advbiocomp.com/licensing/ RepeatMasker 3.2.8 and above fully support both variants ]
- 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 of RepeatMasker is shipped without a database, however
a minimal version of Dfam 3.8 ( root partition ) can be downloaded automatically by
the configure script. Additional taxa partitions may be downloaded and configured
at any time.
- Download RepeatMasker
Latest Released Version: 12/5/23: RepeatMasker-4.1.6.tar.gz
Previous Released Version: 3/23/23: RepeatMasker-4.1.5.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 is currently not distributed with a database. The configure
script will prompt to download a minimal Dfam database during installation.
There are three options for supplementing/updating the main RepeatMasker library:
- The complete Dfam 3.8 database
may be downloaded from www.dfam.org in partitioned famdb HDF5 format
or individual partitions (divided by taxa) may be downloaded as needed.
- wget https://www.dfam.org/releases/Dfam_3.8/families/FamDB/dfam38_full.0.h5.gz
- gunzip dfam38_full.0.h5.gz
- mv dfam38_full.0.h5.gz /usr/local/RepeatMasker/Libraries/famdb
- NOTE: only partitions from the same Dfam release should be in this directory
- 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.
- Upgraded to FamDB 1.0.2 to support Dfam 3.8 and the new partitioned
- Added Libraries/RMRB_spec_to_tax.json to project. This maps the
RepBase taxanames to current NCBI tax_ids and needs to be refreshed
with each new Dfam release.
- Added softmasking support to NCBIBlastSearchEngine.pm.
- Added new '--uncurated' flag to handle single export Dfam format.
If this flag is used the CONS/HMM cached directories will be suffixed
- Fixed sunk error messages from famdb.py. Now they will be displayed
and cause RepeatMasker to quit.
- Additional library setup steps and error checking for configure utility.
- CAF documentation in SearchResult.
- calcDivergenceFromAlign clarified use of "-a" in documentation.
- Updated codebase for Dfam 3.7 compatibility (famdb format 4.3).
- Penelope classification change caused *.tbl file accounting
to place them in the Unknown category. Also fixed landscape
- Added a new utility to merge *.out *.align files generated by
running RepeatMasker serially.
- Repbase metadata was out-of-date, updated species names
so that they match the current NCBI Taxonomy names.
- Fixed an issue with the HMM parser. It wasn't recognizing
negative values for Tau with models that do not have GA thresholds.
- Added support for RMBlast 2.13.0.
- Release of the TE genome browser visualization (UCSC) and trackhub generation tool.
- New CpGSites and unadjusted Kimura stats in the *.align file.
- Fixed a bug that caused the read-only state of the input fasta file to propogate to the intermediate files and cause the program to exit.
- Removed DateRepeats as it's based on old library formats - this functionality will return with the refactored version of RM in the works.
- A recent change in 4.1.3 to correct blank fragment ID fields can in rare
cases causing the error message: 'Can't call method "setLeftLinkedHit"'.
- The RepeatAnnotationData.pm file containing necessary information for
recognizing equivalent fragments of DNA transposons was missing data.
- The MULE-MuDR class was added to the *.tbl file for "-lib" searches.
- A new utility for generating trackHubs for our new UCSC TE visualization
Fix a bug where killing RM while starting up can leave the cached libraries
in an inconsistent state.
- Fixed a bug where in rare cases the joined fragment ID field is blank
- Merged in changes to Dupmasker supporting multi-threaded use
- Fixed legacy RepBase taxonomic labels
- Added support for GFF v3 output and fixed the utility/rmOutToGFF3.pl
- Releases 4.1.1-4.1.2 contained a bug with the processing of Alu sequences in primates. The step
where an initial annotation is refined into a particular Alu subfamily was not performed and the annotations
remained labeled with the initial capture sequence ( AluJb, AluSx, or AluY ). This patch release fixes this
- Fixed 21 protein family classifications in RepeatProteinLib.
- Fixed a problem with the generation of the RepeatMasker.lib file
for use by RepeatModeler. In release 4.1.1 it did not add the
classification info to this auxilary file.
- Fixed a "log(0)" error that can cause the program to fault in rare
- buildSummary now supports FamDB and has improved documentation.
- Bugfixes and improvements to FamDB.
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: 22.214.171.124.10.50.10
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.