EIGENSOFT protocols

View EIGENSOFT computational protocol

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Associated diseases

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EIGENSOFT specifications

Information


Unique identifier OMICS_07868
Name EIGENSOFT
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

Subtool


  • smartpca

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Versioning


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Documentation


Maintainer


  • person_outline Samuela Pollack <>

Publications for EIGENSOFT

EIGENSOFT in pipelines

 (48)
2018
PMCID: 5805289
PMID: 29420653
DOI: 10.1371/journal.pone.0192446

[…] of the populations based on the deleteriousness they harbored for cardiovascular diseases was assessed by principal component analysis (pca) using the plink tool (v1.90b3.30) [] and verified by eigensoft’s smartpca (version 3.0) []., annotation of the variants in genes set related to cardiovascular diseases were carried out using the clinvar data release 20160104 []. the allele frequencies […]

2018
PMCID: 5877975
PMID: 29463742
DOI: 10.1073/pnas.1716839115

[…] d(yoruba, taino; palikur, x), where x is the test population, to test whether any other other native american group in our dataset is more closely related to the taino than the palikur ()., we used eigensoft (102) to calculate pairwise fst distances based on allele frequencies in our dataset. the distance matrix was then used to build a neighbor-joining tree using the ape package in r (). […]

2018
PMCID: 5890276
PMID: 29632299
DOI: 10.1038/s41467-018-03178-z

[…] studies only; http://www.uk10k.org/) as reference. in order to account for genomic inflation post imputation in the german data set, eigenvectors were inferred using the “smartpca” component within eigensoft v2.4 and adjustment was carried out by including the first two eigenvectors as covariates in snptest during association analysis,. the inflation factor λ and λ1000 was again calculated […]

2018
PMCID: 5905515
PMID: 29668959
DOI: 10.1093/gigascience/giy019

[…] 1.02 [], and used the homologous sites of goat to determine the ancestral alleles for each snp. only biallelic autosomal snps were used to calculate the distance matrix. pca was performed using eigensoft, version 6.0.1 [, ], and population structures were inferred using frappe software, version 1.1 []. both the pca and population structures were calculated based on autosomal snps […]

2018
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 […]


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EIGENSOFT in publications

 (426)
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 […]

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 […]

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 […]

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 […]

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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