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The EIGENSOFT package implements methods from the following 2 papers:
- Patterson et al. 2006 PLoS Genet 2:e190 (population structure)
- Price et al. 2006 Nat Genet 38:904-9 (EIGENSTRAT stratification correction)
- New option lsqproject for PCA projection with large amounts of missing data
- New options grmoutname and grmbinary to output genetic relationship matrix, compatible with GCTA software (v1.13)
- Expanded options for LD regression in computing genetic relationship matrix
- Bug fix for PLINK format files with out-of-order SNPs
- NOTE: multi-threading is no longer supported. Users wishing to run in multi-threaded mode are recommended to use EIG4.2
- NOTE: fortran compiler is no longer required to build EIGENSOFT. (However, the lapack and blas libraries must still be installed on the system)
See CONVERTF for documentation of programs for converting file formats. See POPGEN for documentation of population structure programs. See EIGENSTRAT for documentation of EIGENSTRAT programs.
See http://www.hsph.harvard.edu/faculty/alkes-price/files/eigensoftfaq.htm or email Samuela Pollack, spollack@hsph.harvard.edu
We would like to thank John Novembre and Mike Boursnell for code improvements and especially Matt Hanna for the first implementation of multi-threading.
This software and its documentation are copyright (2010) by Harvard University and The Broad Institute. All rights are reserved. This software is supplied without any warranty or guaranteed support whatsoever. Neither Harvard University nor The Broad Institute can be responsible for its use, misuse, or functionality. The software may be freely copied for non-commercial purposes, provided this copyright notice is retained.