Minnesota Supercomputing Institute
4.0.5
4.0.5, 4.0.1, 4.0.3, 4.0.5, 4.1.1
Tuesday, August 29, 2023
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
http://www.repeatmasker.org/