Table 1.

Methods for Detecting and Identifying Archaic Admixture

Method	Publication	Link
Admixfrog	Peter (2021)	https://github.com/BenjaminPeter/admixfrog
ArChie	Durvasula and Sankararaman (2019, 2020)	https://github.com/sriramlab/ArchIE
Conditional Random Field (CRF)	Sankararaman et al. (2014, 2016)
Conditional Site Frequency Spectrum (CSFS)	Durvasula and Sankararaman (2020)
ARGWeaver-D	Hubisz et al. (2020)	https://github.com/CshlSiepelLab/argweaver
Convolutional Neural Network (CNN)	Flagel et al. (2019)	https://github.com/flag0010/pop_gen_cnn
	Gower et al. (2021)	https://github.com/grahamgower/genomatnn
diCal-admix, CSD	Steinrücken et al. (2018)	http://dical-admix.sourceforge.net
HMM	Skov et al. (2018)	https://github.com/LauritsSkov/Introgression-detection/
IBDmix	Chen et al. (2020)	https://github.com/PrincetonUniversity/IBDmix
IMa3	Hey et al. (2018)	https://github.com/jodyhey/IMa3
Legofit	Rogers (2019)	https://github.com/alanrogers/legofit
Moments, moments. LD	Ragsdale and Gravel (2019)	https://bitbucket.org/simongravel/moments/src/master/
Relate	Speidel et al. (2019)	https://myersgroup.github.io/relate/
RD, U, and Q95 Statistics	Racimo et al. (2017)
S*	Plagnol and Wall (2006); Racimo et al. (2015), Vernot and Akey (2014), Vernot et al. (2016)	https://github.com/bvernot/freezing-archer
SPrime	Browning et al. (2018)	https://github.com/browning-lab/sprime
tsinfer	Kelleher et al. (2019)	https://github.com/tskit-dev/tsinfer
VolcanoFinder	Setter et al. (2020)	http://degiorgiogroup.fau.edu/vf.html

Note.—The publication where each method is described is given. Where available, links to code repositories are also provided.