ADMIXTOOOLS version 3.0, 3/11/15 (for Linux and Mac)

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.
qpGraph is not yet released.  

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:
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All C executables are in the bin/ directory.

Note: The executables included in the bin/ were compiled by clang of Mac.

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 have trouble compiling and running our code, try compiling and
running the examples in the examples/ directory. 

If you are unable to run the examples 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. 


Questions?
email Mengyao Zhao, mengyao_zhao@hms.harvard.edu

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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.