URL: https://reich.hms.harvard.edu/software
Proper Citation: Eigensoft (RRID:SCR_004965)
Description: EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker''s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 3.0 on a Linux platform can be downloaded. New features of EIGENSOFT 3.0 include supporting either 32-bit or 64-bit Linux machines, a utility to merge different data sets, a utility to identify related samples (accounting for population structure), and supporting multiple file formats for EIGENSTRAT stratification correction.
Abbreviations: EIGENSOFT
Synonyms: EIGENSOFT Software
Resource Type: software resource, software toolkit
Defining Citation: PMID:17194218, DOI:10.1038/ng1847
Keywords: population genetics, genetics, stratification, variation
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Warning: PCA results may be sensitive to the sample size, population composition, and the number of columns, in which case the results will not be reliable, robust, nor replicable and should not be used to draw conclusions.
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