Difference between revisions of "TreeMix"
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For the basic TreeMix functions of building trees and adding migration, please cite: | For the basic TreeMix functions of building trees and adding migration, please cite: | ||
| − | [http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002967 Pickrell and Pritchard (2012). Inference of population splits and mixtures from | + | [http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002967 Pickrell and Pritchard (2012). Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genetics.] |
| − | genome-wide allele frequency data. PLoS Genetics.] | ||
For the model incorporating known admixture (-cor mig), please cite: | For the model incorporating known admixture (-cor mig), please cite: | ||
| − | [http://www.nature.com/ncomms/journal/v3/n10/full/ncomms2140.html Pickrell et al. (2012). The genetic prehistory of southern Africa. | + | [http://www.nature.com/ncomms/journal/v3/n10/full/ncomms2140.html Pickrell et al. (2012). The genetic prehistory of southern Africa. NatureCommunications.] |
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Revision as of 13:49, 17 February 2016
Description
TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph.
Required Modules
Serial
- treemix
System Variables
- HPC_{{#uppercase:treemix}}_DIR - installation directory
Citation
If you publish research that uses treemix you have to cite it as follows:
For the basic TreeMix functions of building trees and adding migration, please cite: Pickrell and Pritchard (2012). Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genetics.
For the model incorporating known admixture (-cor mig), please cite: Pickrell et al. (2012). The genetic prehistory of southern Africa. NatureCommunications.