GenomeTools is a versatile open-source genome analysis software that includes LTRharvest, an efficient and flexible software tool for de novo detection of LTR retrotransposons. genometools-1.5.10 v1.5.10 was downloaded from www.genometools.org.
LTR_FINDER is an efficient program for finding full-length LTR retrotranspsons in genome sequences. LTR_FINDER_parallel is an open-source program to run LTR_FINDER in parallel. LTR_FINDER_parallel was downloaded from LTR_FINDER_parallel.
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons. LTR_retriever v2.6 was downloaded from LTR_retriever.
Generic Repeat Finder is a C++ program package for detecting terminal inverted repeats (TIRs), terminal direct repeats (TDRs), interspersed repeats, miniature inverted repeat transposable elements (MITEs), and long terminal repeat (LTR) transposons in genomes.
TIR-Learner is an open-source ensemble method for TIR transposable element annotation. TIR-Learner1.19 is a pipeline version converted from TIR-Learner-Rice. The GenericRepeatFinder is used in TIR-Learner as the search engine.
HelitronScanner is a Java program to identify Helitron transposons in genome sequences. HelitronScanner v1.1 was downloaded from HelitronScanner.
TEsorter is a program for accurate classification of TEs.
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