RepeatMasker
Developed by Arian Smit and Robert Hubley
Please refer to: Smit, AFA, Hubley, R. & Green, P "RepeatMasker" at
http://www.repeatmasker.org

IMPORTANT:
The github 'master' branch only contains the source code files for
the latest release of RepeatMasker.  A complete distribution including
the source files, and a copy of the Dfam database (curated families)
may be found at the RepeatMasker website:
http://www.repeatmasker.org/RepeatMasker/

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). Sequence comparisons in RepeatMasker are performed by one of several available alignment programs:

• RMBlast, a variant of NCBI blastn that supports substitution matrices, complexity adjusted scoring and masklevel filtering.
• crossmatch, an efficient implementation of the Smith-Waterman-Gotoh algorithm developed by Phil Green.
• NHMMER, a profile Hidden Markov Model aligner written by Travis Wheeler and Sean Eddy.
• ABBLAST, A blast variant developed by Warren Gish.

See "INSTALL" for instructions on how to install RepeatMasker. See "repeatmaker.help" for a detailed program manual.

Updates of the RepeatMasker program are distributed with a copy of the Dfam database ( www.dfam.org ). Dfam is an "open" databases of Transposable Element seed alignments, profile Hidden Markov Models and consensus sequences.

RepeatMasker is also compatible with the RepBase database managed by the Genetic Information Research Institute and requires a license to use. Up until 2019 we maintained the "Repbase RepeatMasker Edition" libraries as co-editor of RepBase Update. For newer versions of RepBase users will need to use the sequences in FASTA format with RepeatMasker's "-lib" option.

RepeatMasker "open-4.0" and later versions are distributed under the Open Source License. Please read LICENSE file for more information.