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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Latest revision as of 17:56, 10 June 2022
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.
Environment Modules
Run module spider treemix to find out what environment modules are available for this application.
System Variables
- HPC_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.