Repeat Masker for DNA Sequence Analysis

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).

To run this software interactively in a Linux environment run the commands:

module load trf phrap rmblast repeatmasker
RepeatMasker [-options] fasta_seqfiles(s)

Once you have setup your environment, you can use any of the programs directly from the command line. eg

RepeatMasker -help

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