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README

ADMIXTOOLS version 5.1  9/18/18 (for Linux and Mac)

See README.INSTALL for installation info. 

The ADMIXTOOLS package implements 5 methods described in 
Patterson et al. (2012) Ancient Admixture in Human History. Details of the methods and algorithm can be found in this paper.

The package contains 6 programs: 
convertf: See README.CONVERTF for documentation of programs for converting file formats.
qp3Pop: See README.3PopTest for details of running f_3 test. This test can be used as a format test of admixture with 3 populations.
qpBound: See README.3PopTest for details of running qpBound. This test can be used for estimating bounds on the admixture proportions, given 3 populations (2 reference and one target).
qpDstat: See README.Dstatistics for details of running D-statistics. This is a formal test of admixture with 4 populations.
qpF4Ratio: See README.F4RatioTest for details of running F4 ratio estimation. This program computes the admixture proportion by taking the ratio of two f4 tests.
rolloff:  See README.ROLLOFF/ README.ROLLOFF_OUTPUT for details for running rolloff. This program can be used for dating admixture events.
 
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 programs, type
"cd src"
"make clobber"
"make install"      

If you are building on a Mac, you will need gsl and openblas installed. 
"brew install gsl"
"brew install homebrew/science/openblas"
Uncomment the lines in src/Makefile that modify the CFLAGS and LDFLAGS. 

If you have trouble compiling and running our code, try compiling and
running the examples in the examples/ directory. Download the example
datasets from https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/AdmixTools_Example_Data.tar_.gz
and untar in the root AdmixTools directory, creating a subdirectory called ./data. 

"cd examples"
"./mklog"

If you are unable to run the examples successfully, please contact
your system administrator for help, as this is probably systems issue which is
beyond our scope. 

Nick Patterson
<nickp@broadinstitute.org>

----------------------------
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.
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