REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
Gencode V26, Transcript sequences fasta	Frankish et al.29	https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.transcripts.fa.gz
Gencode M25, Transcript sequences fasta, reference genome fasta	Frankish et al.29	https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25
Pan_tro 3.0, ncRNA, cDNA, reference DNA	Cunningham et al.30	https://ftp.ensembl.org/pub/release-104/fasta/pan_troglodytes/
Mouse Muscle Dataset	Terry et al.17	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100505
Chimp Brain Dataset	Sousa et al.18	https://doi.org/10.7303/syn7067053
Software and algorithms
Terminus v 0.1.0	Sarkar et al.14	https://github.com/COMBINE-lab/Terminus
Salmon v 1.5.2	Patro et al.9	https://github.com/COMBINE-lab/salmon
PySAT v 0.1.7.dev19	Ignatiev et al.31	https://github.com/pysathq/pysat
Snakemake v 6.6.1	Mölder et al.32	https://github.com/snakemake/snakemake
bedtools v 2.29.1	Quinlan and Hall33	https://github.com/arq5x/bedtools2
fastqc v 0.11.7	Andrews et al.34	https://github.com/s-andrews/FastQC
multiqc v 1.8.dev0	Ewels et al.35	https://github.com/ewels/MultiQC
R Packages	This study	https://doi.org/10.5281/zenodo.7807370
TreeTerminus	This study	https://github.com/COMBINE-lab/TreeTerminus/