RepeatMasker v4.0.7

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker on BlueBEAR are performed RMBlast.

Accessing the software

To load the module:

$ module load RepeatMasker/4.0.7-iomkl-2018a

To view a list of command-line options, run the following command:

RepeatMasker -help

RepeatMasker uses the RepBase libraries from These libraries have strict licence conditions restricting their use to a particular research group. If your research group doesn't have access to RepeatMasker then you can request access from the IT Service Desk selecting the "License Server Request" option.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

Previous versions of this application are recorded below:

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the RepeatMasker website for more information regarding this application.

Last modified: 21 June 2018