TreeMix¶

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.

Environment Variables¶

HPC_TREEMIX_DIR - installation directory
HPC_TREEMIX_BIN - executable 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.

Categories¶

biology, phylogenetics