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A repeat-detection tool capable of labeling its training data and training itself automatically on an entire genome. Red is easy to install and use. It is sensitive to both transposons and simple repeats; in contrast, available tools such as RepeatScout and ReCon are sensitive to transposons, and WindowMasker to simple repeats. Red performed consistently well on seven genomes; the other tools performed well only on some genomes. Red is much faster than RepeatScout and ReCon and has a much lower false positive rate than WindowMasker.

Software type:
Command line interface
Restrictions to use:
Operating system:
Unix/Linux, Mac OS
Programming languages:
Computer skills:
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2 user reviews

zico's avatar image


The author new email is: [email protected]. Feel free to contact the author about Red.

Diablo's avatar image


This tool looks pretty user-friendly. However, I did exactly what the manual says, and never got it to…

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  • Hani Z. Girgis <girgishz at mail.nih.gov>


Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda 20894, MD, USA; Tandy School of Computer Science, University of Tulsa, 800 South Tucker Drive, Tulsa 74104, OK, USA

  • (Girgis, 2015) Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. BMC bioinformatics.
    PMID: 26206263
  • (Bergman and Quesneville, 2007) Discovering and detecting transposable elements in genome sequences. Briefings in bioinformatics.
    PMID: 17932080
  • (Lerat, 2010) Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity.
    PMID: 19935826
  • (Janicki et al., 2011) Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes. Chromosome research.
    PMID: 21850457
  • (Hoen et al., 2015) A call for benchmarking transposable element annotation methods. Mobile DNA.
    PMID: 26244060

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