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README
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EIGENSOFT version 5.0, 07/15/13 (for Linux only)
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 features of EIGENSOFT version 5.0 include (see POPGEN/README):
-- 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/README for documentation of programs for converting file formats.
See POPGEN/README for documentation of population structure programs.
See EIGENSTRAT/README for documentation of EIGENSTRAT programs.
Questions?
See http://www.hsph.harvard.edu/faculty/alkes-price/files/eigensoftfaq.htm
or email Samuela Pollack, [email protected]
Executables and source code:
----------------------------
All C executables are in the bin/ directory.
We have placed source code for all C executables in the src/ directory,
for users who wish to modify and recompile our programs. For example, to
recompile the eigenstrat program, type
"cd src"
"make eigenstrat"
"mv eigenstrat ../bin"
Note that some of our software will only compile if your system has the
lapack package installed. (This package is used to compute eigenvectors.)
Some users may need to change "blas-3" to "blas" in the Makefile,
depending on how blas and lapack are installed.
If you have trouble compiling and running our code, try compiling and
running the pcatoy program in the src directory:
"cd src"
"make pcatoy"
"./pcatoy"
If you are unable to run the pcatoy program successfully, please contact
your system administrator for help, as this is a systems issue which is
beyond our scope. Your system administrator will be able to troubleshoot
your systems issue using this trivial program. [You can also try running
the pcatoy program in the bin directory, which we have already compiled.]
To remake the entire package:
"cd src"
"make clobber"
"make install"
----------------------------
Acknowledgements:
We would like to thank John Novembre and Mike Boursnell for code improvements
and especially Matt Hanna for the first implementation of multi-threading.
----------------------------
SOFTWARE COPYRIGHT NOTICE AGREEMENT
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.