Table 1 Commonly applied algorithms to SNP data for quantifying individual population substructure in humans

Model-free

Principal component analysis

EIGENSOFT^a

http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html

[70]

Principal components and Moran’sI

adegenet (R software)

http://adegenet.r-forge.r-project.org/

[71]

Multidimensional scaling

PLINK^a

http://pngu.mgh.harvard.edu/~purcell/plink/

[28]

Principal coordinates

PCO-MC

http://lamar.colostate.edu/~reevesp/PCOMC/PCOMC.html

[72]

Spectral graph theory

GemTools

http://wpicr.wpic.pitt.edu/WPICCompGen/GemTools/GemTools.htm

[43]

Spectral graph theory

SpectralGem

http://wpicr.wpic.pitt.edu/WPICCompGen/Spectral-GEM/GEM+.htm

[56]

Laplacian eigenfunction

LAPSTRUCT

http://galton.uchicago.edu/~junzhang/LAPSTRUCT.html

[57]

Genetic algorithm coupled to AMOVA

GAGA

http://www.erasmusmc.nl/fmb/resources/GAGA/

[73]

Model-based

Log-likelihood HWE

ADMIXTURE

https://www.genetics.ucla.edu/software/admixture/

[24]

Log-likelihood HWE

FRAPPE

http://med.stanford.edu/tanglab/software/frappe.html

[31]

Bayesian HWE

STRUCTURE

http://pritchardlab.stanford.edu/structure.html

[22]

Bayesian HWE

fastSTRUCTURE

http://pritchardlab.stanford.edu/structure.html

[59]

Nonnegative matrix factorization

sNMF

http://membres-timc.imag.fr/Eric.Frichot/snmf/index.htm

[25]

Bayesian

BAPS

http://www.helsinki.fi/bsg/software/

[74]

Chromopainting and Bayesian classifier

fineSTRUCTURE

http://www.paintmychromosomes.com

[60]

Log-likelihood genotypic/haplotypic gradients

LOCO-LD

http://loco.icsi.berkeley.edu/loco/

[37]

Log-likelihood allelic gradients

SPA

http://genetics.cs.ucla.edu/spa/

[36]

ADMIXTURE and linear regression

GPS

http://chcb.saban-chla.usc.edu/gps/

[39]

Bayesian clustering with spatial information

TESS

http://membres-timc.imag.fr/Olivier.Francois/tess.html

[38]