PopCluster is a computer program created and maintained by Jinliang Wang. It implements several maximum likelihood methods based on mixture and admixture models to make unsupervised population structure analysis from the marker genotype data of a sample of individuals.

It can be used to infer the most likely number of populations represented by a sample of individuals, assign the sampled individuals to source populations, estimate each individual's admixture proportions, estimate an individual's hybrid classes, and estimate the migration rates and Ne of each assumed population.

The program was created (version in year 2020. The current version ( of PopCluster has the following features:

Running on all major platforms, Windows, Linux and Mac;

  • Applicable to both multiallelic markers (e.g. microsats) and diallelic markers (e.g. SNPs);
  • Implementing multiple models for clustering analysis, admixture analysis, hybridization analysis and migration analysis;
  • Implementing efficient algorithms to handle many GBs of genomic data (say millions of SNPs or/and individuals);
  • Capable of MPI parallel runs to employ many cores and distributed memory in a cluster;
  • Allowing openMP parallel threads within an MPI parallel process;
  • Integrating GUI for visualizing admixture and other results (Windows version only);
  • Integrating a simulation module to generate mixture, admixture, hybridization and migration genotype data.

The PopCluster download form: