- 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
- Repeat Database
RepeatMasker will now work with custom libraries, Dfam, and with Dfam_consensus
out of the box. Dfam is a database of Transposable Element profile HMM models.
The current release ( Dfam2.0 ) contains 4,150 models
spanning five organisms: human, mouse, zebrafish, fruit fly,
and nematode. Dfam_consensus is a new open database of Transposable Element consensus
sequences. To supplement these growing 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
To obtain updated Dfam_consensus and RepeatMasker metadata click