EIGENSOFT statistics

Tool stats & trends

Looking to identify usage trends or leading experts?


EIGENSOFT specifications


Unique identifier OMICS_07868
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 6.0.1
Stability Stable
Maintained Yes


  • smartpca




No version available



  • person_outline Samuela Pollack

Publications for EIGENSOFT

EIGENSOFT citations


Genetic variant for behavioral regulation factor of executive function and its possible brain mechanism in attention deficit hyperactivity disorder

Sci Rep
PMCID: 5956073
PMID: 29769613
DOI: 10.1038/s41598-018-26042-y
call_split See protocol

[…] (4) with relatives having genome identity PI_HAT ≥ 0.185 were removed. Then, the remaining samples were assessed for population stratification using Principal Component Analysis (PCA) implemented in EIGENSOFT4.2,. Tracy-Widom test was employed to detect significant eigenvectors (P < 0.05). Only the first eigenvector (eigenvector 1) was significant, which was used as a covariate in the subsequent […]


Analysis of the canid Y chromosome phylogeny using short read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs

BMC Genomics
PMCID: 5946424
PMID: 29747566
DOI: 10.1186/s12864-018-4749-z

[…] Autosomal genetic ancestry was visualized via a principal components analysis (PCA) using the smartPCA program from eigensoft version 3.0 []. For the PCA, we limited variants to those present on the 170 K Illumina HD Canine SNP Array so that the larger collection of samples from Shannon et al. […]


Nonparametric approaches for population structure analysis

Hum Genomics
PMCID: 5944014
PMID: 29743099
DOI: 10.1186/s40246-018-0156-4
call_split See protocol

[…] tructure, where the most genetically isolated subpopulations appear as distinct clusters of individuals. Most importantly, PCA can be used to infer spatial population genetic variations [].EIGENSTRAT\smartpca [, ] is the most used PCA-based tool for detecting population structure. In EIGENSTRAT\smartpca, eigenanalysis is used to detect population substructure, such that eigenvalues and eigenvector […]


Comparative genomic analysis of multidrug resistant Streptococcus pneumoniae isolates

PMCID: 5939923
PMID: 29765237
DOI: 10.2147/IDR.S147858

[…] or each method, 1,000 bootstrap replicates provided support for nodes on the tree. The phylogenies derived from each method were congruent. We conducted principal component analysis on the SNPs using EIGENSOFT 5.02, and the eigenvectors were obtained from the covariance matrix using the R function. […]


Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species

PMCID: 5932900
PMID: 29720271
DOI: 10.1186/s40168-018-0467-7

[…] model [] and employed 999 permutations to estimate the probability of homogeneity. In order to further assess population genetic structure, we conducted a principal component analysis (PCA) using the smartPCA program in the Eigensoft package []. The datasets were reduced to ten eigenvectors, and the principal components 1 and 2 as well as 1 and 3 were plotted using the Perl script Ploteig (Eigenso […]


Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans

Nat Commun
PMCID: 5931558
PMID: 29717136
DOI: 10.1038/s41467-018-03857-x

[…] als in the 1000 Genomes data set (release 20130502). Genotypes with alleles other than those observed in the European samples from the 1000 Genomes project were excluded as likely errors. We used the smartpca software (v13050) with default parameters for outlier detection (numoutlierevec 10, outliersigmathresh 6) to conduct the PCA. Overall, 463 of 503 European samples from the 1000 Genomes projec […]


Looking to check out a full list of citations?

EIGENSOFT institution(s)
Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA


star_border star_border star_border star_border star_border
star star star star star

Be the first to review EIGENSOFT