Key resources table

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Bacterial and virus strains
Biological samples
Whale sequencing reads	Westbury et al., 2021	Table S4
Bee sequencing reads	Sun et al., 2021	Table S5
Drosophila sequencing reads	Miller et al., 2018	Table S6
Lice sequencing reads	Boyd et al., 2017	Table S7
Chemicals, peptides, and recombinant proteins
Critical commercial assays
Deposited data
Experimental models: Cell lines
Experimental models: Organisms/strains
Oligonucleotides
Recombinant DNA
Experimental models: Cell lines
Recombinant DNA
Software and algorithms
Skmer code	This paper	https://github.com/shahab-sarmashghi/Skmer
ART	Huang et al., 2012	https://www.niehs.nih.gov/research/resources/software/biostatistics/art/
Seqtk	N/A	https://github.com/lh3/seqtk
Kraken2	Wood et al., 2019	https://github.com/DerrickWood/kraken2
Bowtie2	Langmead et al., 2019	https://sourceforge.net/projects/bowtie-bio/files/bowtie2/
CONSULT	Rachtman et al., 2021	https://github.com/noraracht/CONSULT
BBTools	Bushnell et al., 2017	https://sourceforge.net/projects/bbmap/files/
INDELible	Fletcher and Yang, 2009	http://abacus.gene.ucl.ac.uk/software/indelible/
FastME	Lefort et al., 2015	http://www.atgc-montpellier.fr/fastme/
RAxML	Stamatakis, 2014	https://github.com/stamatak/standard-RAxML
RepeatMasker	N/A	http://www.repeatmasker.org/
Other
Data and summary of analyses	This paper	https://github.com/noraracht/subsample_support_scripts https://doi.org/10.5281/zenodo.6473473