Software and Databases

Most of our software packages can be installed via conda

PrinTE forward simulation of TE insertions and deletions (bioRxiv)

AnnoSINE_v2 de novo SINE annotation in plant and animal genomes (Mob. DNA)

TIR-Learner_v3 de novo annotation of TIR DNA transposons in eukaryotic genomes

panEDTA pangenome EDTA for consistent and high-quality annotation of TEs (example: PopTEvo; Genome Res.)

EDTA Extensive de-novo TE Annotator for structural and homology annotation of TEs (Genome Bio.)

TEsorter an accurate and fast method to classify LTR retrotransposons in plant genomes (Hort. Res.)

LAI the LTR Assembly Index for evaluation of repeat assembly in genomes (Nucleic Acids Res.)

LTR_HARVEST_parallel a multi-threaded wrapper for LTRharvest

LTR_FINDER_parallel a multi-threaded wrapper for LTR_FINDER (Mob. DNA)

LTR_retriever a highly accurate and sensitive program for identification of LTR retrotransposons (Plant Phys.)

ThetaPi estimate nucleotide diversity using tabular population SNPs

riceTElib a collection of manually curated TE examplars in rice (Oryza sativa).

MTEC a collection of historical and updated TE libraries from the Maize TE Consortium.