TE data across DToL public data

This repository contains RepeatModeler consensus repeat libraries for hundreds of species from the Darwin Tree of Life (DToL) / Ensembl repeats FTP.

These data are useful for exploring:

• transposable element (TE) diversity
• genome repeat composition
• comparative genomics across species

Directory structure

# data for each species is in the `data` directory
data/<species>/<assembly_accession>/
# example
data/zygaena_filipendulae/GCA_907165275.1

Inside each assembly directory:

folder	contents
input/	original RepeatModeler FASTA + classified FASTA
logs/	RepeatClassifier logs
results/	processed outputs
work/	temporary working files

The most important file is:

input/<assembly>.repeatmodeler.fa.classified

This contains consensus repeat sequences with annotations where possible.

What is a RepeatModeler consensus?

RepeatModeler identifies repeated DNA sequences in a genome and builds a consensus sequence for each repeat family.

Each FASTA entry represents one repeat family.

e.g.

>rnd-3_family-26#DNA/hAT

Meaning:

• rnd-3 -> discovery round in RepeatModeler
• family-26 -> family ID
• DNA/hAT -> inferred repeat class

If no class is known:

>rnd-6_family-991#Unknown

Later rounds often contain rarer or harder-to-classify repeats.