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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

PMCID: 5956073
PMID: 29769613
DOI: 10.1038/s41598-018-26042-y

[…] (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 […]


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

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

[…] called as potentially recurrent and is incompatible with the phylogenetic tree., 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. [] could […]


Comparative genomic analysis of multidrug resistant Streptococcus pneumoniae isolates

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

[…] 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., the detailed epidemiological data from the selected s. pneumoniae clinical isolates are summarized […]


The genetic architecture of floral traits in the woody plant Prunus mume

PMCID: 5923208
PMID: 29703940
DOI: 10.1038/s41467-018-04093-z

[…] pair of snps and their corresponding correlation coefficient (r2) value. the distance that the ld decays to half of the highest value was then calculated. principle component analysis were taken by eigensoft software using genome-wide snp., nine mei and three prunus varieties were subjected to deep sequencing (~70.1×) using a single paired-end library and a mate-paired library with insert sizes […]


Genome Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds

PMCID: 5902979
PMID: 29692799
DOI: 10.3389/fgene.2018.00118

[…] matrix (). then, the distances were used to construct a nj tree with 1000 bootstraps using the package phylip v.3.695 (). in addition, pca was conducted using the smartpca program from the eigensoft package version 4.2 () based on the genotypes data., to explore genetic structure within the breeds, multidimensional scaling (mds) analysis was performed based on the independent snps […]


Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater

PMCID: 5893588
PMID: 29636446
DOI: 10.1038/s41467-018-03722-x

[…] (nj) method implemented in vcf-kit (http://vcf-kit.readthedocs.io/) and maximum-likelihood (ml) method using raxml (version 7.2.3). the principal component analysis (pca) was conducted using eigensoft3.0 and the significance of eigenvectors were determined with the tracey–widom test. fdist was used to determine presumably neutral snps for pca analyses and phylogeny reconstruction. […]

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


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