EIGENSOFT version 3.0, 04/21/09 (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 3.0 include:
-- Supporting 64-bit machines, with unlimited file sizes
-- A utility to merge different data sets, intersecting the SNP sets
-- A utility to identify related samples, accounting for population structure
-- Supporting multiple file formats for EIGENSTRAT stratification correction

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, spollack@hsph.harvard.edu

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.]