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CLARI-TE specifications


Unique identifier OMICS_13534
Software type Package/Module
Interface Command line interface
Restrictions to use License purchase required
Input data The xm output file of RepeatMasker, a tabular file containing the classification of the library use in RepeatMasker, a tabular file containing the position of the LTR retrotransposons present in the library, embl file containing the gene annotation of the sequence (in triAnnot format), a FASTA-format file containing your query sequence.
Input format XM, FASTA
Output data Prediction
Output format EMBL
Operating system Unix/Linux
Programming languages Perl
License CeCILL version 2.1
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes


  • Plants and Fungi
    • Triticum aestivum


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  • person_outline Josquin Daron

Publication for CLARI-TE

CLARI-TE citation


The case for not masking away repetitive DNA

PMCID: 5930866
PMID: 29743957
DOI: 10.1186/s13100-018-0120-9

[…] assay repetitive DNA from whole genome data. These tools include MELT, RetroSeq, EpiTEome and McClintock for TE insertion site identification [–], T-lex to identify presence/absence of TE copies [], Clari-TE to resolve nested TE structure [], TEtoolkit/TEtranscripts for TE enrichment analysis from experiments such as RNA-seq and ChIP-seq [, ], and many others. Which tool to use is specific to the […]

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CLARI-TE institution(s)
INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France; University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France; INRA-URGI, Centre de Versailles, Versailles, France; CEA/DSV/IG/Genoscope, Evry, France; CNRS UMR 8030, Evry, France; Université d’Evry, Evry, France
CLARI-TE funding source(s)
This project was supported by grants from the French National Research Agency (ANR-09-GENM-025 3BSEQ), a grant from France Agrimer, a grant (project DL-BLE) from the INRA BAP division; and partly by a grant from the French Ministry of Research, by a grant from the European Commission research training program Marie-Curie Actions (FP7-MC-IIF-NoncollinearGenes) and by a grant from the Region Auvergne.

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