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