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RepeatModeler

RepeatModeler

RepeatModeler is a tool to find transposable elements and consists of three programs to compute repeat boundaries and classify family relationships from DNA sequence data sets:
RECONRepeatScoutLtrHarvest/Ltr_retriever

Topic

Sequence composition, complexity and repeats; Sequence composition, complexity and repeats

Details

  • Operation: Repeat sequence detection
  • Software interface: Command-line user interface
  • Language: Perl
  • Operating system: Linux
  • License: Creative Commons Zero v1.0 Universal ; Open Source License v2.1
  • Cost: Free
  • Version name: 2.0.1
  • Credit: NIH, National Human Genome Research Institute, Natural Sciences and Engineering Research Council of Canada, National Institute of General Medical Sciences
  • Contact: rhubley _at_ systemsbiology.org
  • Collection: -

Publications

Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, Smit AF "RepeatModeler2 for automated genomic discovery of transposable element families" Proc Natl Acad Sci U S A. 2020 Apr 28;117(17):9451-9457 https://doi.org/10.1073/pnas.1921046117
PMID: 32300014
PMCID: PMC7196820


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