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<meta name="description" content="The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary.">
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<meta name="keywords" content="genome analysis, GFF3, genome annotation,
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annotation drawing, AnnotationSketch, LTR prediction, bioinformatics, computational biology">
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<li><a id="current" href="index.html">Overview</a></li>
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<li><a href="pub/">Download</a></li>
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<li><a href="cgi-bin/gitweb.cgi?p=genometools.git;a=summary">Browse source</a></li>
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<li><a href="http://genometools.lighthouseapp.com/">Issue tracker</a></li>
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<li><a href="libgenometools.html">C API</a></li>
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<li><a href="docs.html"><tt>gtscript</tt> docs</a></li>
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<li><a href="annotationsketch.html"><tt>AnnotationSketch</tt></a></li>
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<li><a href="/cgi-bin/gff3validator.cgi">GFF3 validator</a></li>
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<li><a href="license.html">License</a></li>
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<h1><i>GenomeTools</i></h1>
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<h3>The versatile open source genome analysis software</h3>
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<p id="examplesketch" >
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<a href="annotationsketch.html">
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<img src="images/annotation.png" alt="[Genome Annotation]">
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The <i>GenomeTools</i> genome analysis system is a <a
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href="license.html">free</a> collection of bioinformatics tools (in the realm of
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genome informatics) combined into a single binary named <tt>gt</tt>.
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It is based on a C library named “libgenometools” which consists of
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If you are interested in gene prediction, have a look at
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<a href="http://genomethreader.org" title="GenomeThreader gene prediction
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software"><i>GenomeThreader</i></a>.
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<i>GenomeTools</i> has been designed to run on every
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<a href="http://en.wikipedia.org/wiki/POSIX">POSIX</a> compliant
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<a href="http://en.wikipedia.org/wiki/UNIX">UNIX</a> system. For example, Linux,
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Mac OS X, and OpenBSD. A <a href="pub/binary_distributions">Windows version</a> which
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requires a <a href="http://www.cygwin.com/">Cygwin</a> installation
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is available. Please report problems with it to our
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<a href="mailman/listinfo/gt-users">mailing list</a>.
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<h2>Published software in <em>GenomeTools</em></h2>
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The <em>GenomeTools</em> distribution includes several published software
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<li><tt><a href="http://www.zbh.uni-hamburg.de/LTRharvest">ltrharvest</a></tt>, an efficient and flexible software tool for
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<em>de novo</em> detection of LTR retrotransposons.
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D. Ellinghaus, S. Kurtz, and U. Willhoeft.<br>
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<i>LTRharvest</i>, a efficient and flexible software for <i> de novo </i>
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detection of LTR retrotransposons. <br>
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<a href="http://www.biomedcentral.com/1471-2105/9/18/abstract">
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BMC Bioinformatics 2008, 9:18
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<li><tt><a href="http://www.zbh.uni-hamburg.de/tallymer">tallymer</a></tt>, a collection of flexible and memory-efficient
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programs for <em>k</em>-mer counting and indexing of large sequence sets.
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S. Kurtz, A. Narechania, J.C. Stein, and D. Ware.<br>
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A new method to compute K-mer frequencies and its application to annotate
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large repetitive plant genomes.<br>
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<a href="http://www.biomedcentral.com/1471-2164/9/517/abstract">
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BMC Genomics 2008, 9:517
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<li><tt>uniquesub</tt>, a program for computing minimum unique substrings.
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S. Gräf, F.G.G. Nielsen, S. Kurtz, M.A. Huynen, E. Birney,
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H. Stunnenberg, and P. Flicek.<br>
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Optimized design and assessment of whole genome tiling arrays.<br>
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<a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i195">
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Bioinformatics 2007, 23(13):i195–i204
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<li><tt>AnnotationSketch</tt>, a library for drawing genome annotations.
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S. Steinbiss, G. Gremme, C. Schärfer, M. Mader and S. Kurtz.<br>
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<em>AnnotationSketch</em>: a genome annotation drawing library.<br>
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<a href="http://bioinformatics.oxfordjournals.org/cgi/content/short/25/4/533">
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Bioinformatics 2009, 25(4):533–534
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<li><tt><a href="http://www.zbh.uni-hamburg.de/LTRdigest">ltrdigest</a></tt>, a software tool for automated annotation of internal features of LTR retrotransposons.
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S. Steinbiss, U. Willhoeft, G. Gremme and S. Kurtz.<br>
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Fine-grained annotation and classification of <em>de novo</em> predicted LTR retrotransposons.<br>
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<a href="http://nar.oxfordjournals.org/cgi/content/full/37/21/7002">
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Nucleic Acids Research 2009, 37(21):7002–7013
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<li><tt><a href="http://www.zbh.uni-hamburg.de/mgth">MetaGenomeThreader</a></tt>, a software to predict genes, such as PCS's (predicted coding sequences) in sequences of metagenome projects.
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D.J. Schmitz-Hübsch and S. Kurtz.<br>
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MetaGenomeThreader: A software tool for predicting genes in DNA-sequences of metagenome projects.<br>
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In R. Daniel and W. Streit (Eds.), <em>Metagenomics. Methods in Molecular Biology</em>, 325–338, Humana Press, Totowa, NJ, ISBN 978-1-60761-822-5
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<li><i><a href="http://www.zbh.uni-hamburg.de/encseq">GtEncseq</a></i>, a compressed biosequence representation with many features.
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S. Steinbiss and S. Kurtz.<br>
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A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences.<br>
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<a href="http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.146">
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IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012, 9(2):345–357
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The <em>GenomeTools</em> are being developed by: <br />
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Gordon Gremme, Sascha Steinbiss, Stefan Kurtz and <a href="/cgi-bin/gitweb.cgi?p=genometools.git;a=blob;f=CONTRIBUTORS;hb=HEAD">others</a><br />
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<a href="http://www.zbh.uni-hamburg.de/research/GI">Genome Informatics Research Group</a><br />
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<a href="http://www.zbh.uni-hamburg.de">Center for Bioinformatics, University of Hamburg</a>
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Copyright © 2006-2011
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<a href="mailto:gremme@gmail.com">Gordon Gremme.</a> Last update: 2011-11-09
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