Difference between revisions of "AdmixTools"
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| − | + | [http://genetics.med.harvard.edu/reich/Reich_Lab/Software_files/2012_Patterson_AncientAdmixture_Genetics.pdf N. Patterson et al. ''Genetics'', vol 192:'''1065–1093'''] | |
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Revision as of 17:10, 19 June 2015
Description
ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.
Required Modules
Serial
- AdmixTools
Parallel (OpenMP)
- intel
- AdmixTools
Parallel (MPI)
- intel
- openmpi
- AdmixTools
System Variables
- HPC_{{#uppercase:AdmixTools}}_DIR - installation directory
Additional Information
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.
Citation
If you publish research that uses AdmixTools you have to cite it as follows:
N. Patterson et al. Genetics, vol 192:1065–1093