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#### Introduction

nested (now also called TE-greedy) is software to analyze nested LTR transposable elements 
in DNA sequences, such as reference genomes. It is made of two components: nested-generator 
for generating simulated sequences of nested retrotransposons, and nested-nester (now called 
TE-greedy-nester) that looks for nested, as well as non-nested and solo-LTR repeat sequences 
in the input. Unlike other similar software, TE-greedy-nester is structure-based by using 
de-novo retrotransposon identification software LTR Finder, relying on sequence information 
*nested* (now also called *TE-greedy*) is software to analyze nested LTR transposable elements 
in DNA sequences, such as reference genomes. It is made of two components: *nested-generator* 
for generating simulated sequences of nested retrotransposons, and *nested-nester* (now called 
*TE-greedy-nester*) that looks for nested, as well as non-nested and solo-LTR repeat sequences 
in the input. Unlike other similar software, *TE-greedy-nester* is structure-based by using 
de-novo retrotransposon identification software *LTR Finder*, relying on sequence information 
only secondarily.

#### External tools