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A software pipeline to analyze transposable elements (TE) insertions in next-generation sequencing (NGS) data data. T-lex allows users to accurate genotyping of individual TE insertions and get the estimation of their population frequencies both using individual strain and pooled NGS. To achieve this, T-lex uses information from (i) a module specifically designed to identify target site duplications and (ii) the genomic context of each insertion, to identify putatively miss-annotated TE insertions. T-lex2 is composed of five modules that can be run with individual strain or pooled NGS datasets.

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2 user reviews

2 user reviews

Kate's avatar image


I am using for my population sequencing data and this tool is very useful. thanks.

Mike's avatar image


Lot of features for TE genotyping. Very useful!

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T-lex classification

T-lex specifications

Software type:
Restrictions to use:
Operating system:
GNU General Public License version 2.0
Command line interface
Output data:
Frequency of the analyzed transposable elements
Programming languages:
Computer skills:

T-lex distribution


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T-lex support



  • asfiston <>


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Department of Biology, Stanford University, Stanford, CA, USA; Institut des Sciences de l’Evolution de Montpellier (ISEM), UMR5554 CNRS-Universite Montpellier, France; Genomics, Bioinformatics and Evolution Group, Institut de Biotecnologia i de Biomedicina - IBB/Department of Genetics and Microbiology, Campus Universitat Autonoma de Barcelona, Bellaterra, Spain; Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain

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