GenomeTools 1.5.8 – Genome Analysis Software

GenomeTools 1.5.8


GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt.



RESEARCH GROUP FOR GENOME INFORMATICS ,Center for Bioinformatics, University of Hamburg




  • Linux / Mac OsX /Windows with Cygwin


GenomeTools ; for Windows


The GenomeTools distribution includes several published software tools:

  • ltrharvest, an efficient and flexible software tool for de novo detection of LTR retrotransposons.
    D. Ellinghaus, S. Kurtz, and U. Willhoeft.
    LTRharvest, a efficient and flexible software for de novo detection of LTR retrotransposons.
    BMC Bioinformatics 2008, 9:18
  • tallymer, a collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets.
    S. Kurtz, A. Narechania, J.C. Stein, and D. Ware.
    A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.
    BMC Genomics 2008, 9:517
  • uniquesub, a program for computing minimum unique substrings.
    S. Gräf, F.G.G. Nielsen, S. Kurtz, M.A. Huynen, E. Birney, H. Stunnenberg, and P. Flicek.
    Optimized design and assessment of whole genome tiling arrays.
    Bioinformatics 2007, 23(13):i195–i204
  • AnnotationSketch, a library for drawing genome annotations.
    S. Steinbiss, G. Gremme, C. Schärfer, M. Mader and S. Kurtz.
    AnnotationSketch: a genome annotation drawing library.
    Bioinformatics 2009, 25(4):533–534
  • ltrdigest, a software tool for automated annotation of internal features of LTR retrotransposons.
    S. Steinbiss, U. Willhoeft, G. Gremme and S. Kurtz.
    Fine-grained annotation and classification of de novo predicted LTR retrotransposons.
    Nucleic Acids Research 2009, 37(21):7002–7013
  • MetaGenomeThreader, a software to predict genes, such as PCS’s (predicted coding sequences) in sequences of metagenome projects.
    D.J. Schmitz-Hübsch and S. Kurtz.
    MetaGenomeThreader: A software tool for predicting genes in DNA-sequences of metagenome projects.
    In R. Daniel and W. Streit (Eds.), Metagenomics. Methods in Molecular Biology, 325–338, Humana Press, Totowa, NJ, ISBN 978-1-60761-822-5
  • GtEncseq, a compressed biosequence representation with many features.
    S. Steinbiss and S. Kurtz.
    A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012, 9(2):345–357
  • Readjoiner, a sequence assembler based on the assembly string graph framework.
    G. Gonnella and S. Kurtz.
    Readjoiner: a fast and memory efficient string graph-based sequence assembler.
    BMC Bioinformatics 2012, 13:82

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