REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
241-way mammalian HAL alignment	Armstrong et al.13	https://cglgenomics.ucsc.edu/data/cactus/
Dfam family database (version 3.6)	Wheeler et al.10	https://www.dfam.org/
Enhanced TE annotations	This paper	Zenodo: https://doi.org/10.5281/zenodo.7716408
RepeatMasker outputs	This paper	Zenodo: https://doi.org/10.5281/zenodo.7716408
SINEBase	Vassetzky el al.17	https://sines.eimb.ru
The human candidate cis-regulatory elements (cCREs) data (registry V3)	ENCODE Project Consortium18	https://screen.encodeproject.org/index/cversions
ENCODE TF ChIP-seq peaks	ENCODE Project Consortium42	Data S3
Human embryo RNA-seq data	Zou et al.28	GEO: GSE197265
Software and algorithms
Code for enhancing TE annotation of a Eutherian genome	This paper	Zenodo: https://doi.org/10.5281/zenodo.7716408
RepeatMasker (version 4.1.2-p1)	Smit et al.8	http://www.repeatmasker.org; RRID:SCR_012954
HAL tools (version 2.1)	Hickey et al.14	https://github.com/ComparativeGenomicsToolkit/hal
BLAST+ (version 2.14.0)	Camacho et al.43	https://blast.ncbi.nlm.nih.gov/Blast.cgi; RRID:SCR_004870
bedtoolsr (version 2.30.0-1)	Patwardhan et al.44	https://github.com/PhanstielLab/bedtoolsr
HMMER (version 3.3.2)	Wheeler et al.45	http://hmmer.org; RRID:SCR_005305
bedtools (version 2.30.0)	Quinlan et al.46	https://bedtools.readthedocs.io/en/latest/; RRID:SCR_006646
MAFFT (version 7.508)	Katoh et al.47	https://mafft.cbrc.jp/alignment/software/; RRID:SCR_011811
Jalview (version 2.11.2.6)	Waterhouse et al.48	https://www.jalview.org/; RRID:SCR_006459
pyTEnrich (version 0.6)	Alexandre Coudray	https://alexdray86.github.io/pyTEnrich/build/html/index.html
STAR (version 2.7.10b)	Dobin et al.49	https://github.com/alexdobin/STAR; RRID:SCR_004463
StringTie (version 2.2.1)	Pertea et al.50	https://github.com/gpertea/stringtie; RRID:SCR_016323
TransDecoder (version 5.7.1)	Haas51	https://github.com/TransDecoder/TransDecoder; RRID:SCR_017647
ggsashimi (version 1.1.5)	Garrido-Martín et al.52	https://github.com/guigolab/ggsashimi