TreeMix

Description

treemix website  

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: [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.]

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. Nature Communications.]