What is at this website?

Software

1. ChromoPainter, for generating a powerful measure of genetic similarity between individuals, performing ADMIXTURE dating, and many other applications.
2. FineSTRUCTURE, a population clustering algorithm for large genomic datasets making use of ChromoPainter.
3. ChromoCombine, for combining multiple ChromoPainter runs (e.g. from a parallel run) and preprocessing for FineSTRUCTURE.
4. Some Useful conversion/processing scripts.
5. Some R scripts for plotting and working with FineSTRUCTURE I/O.
6. Greedy Optimisation bash script for running FineSTRUCTURE on very large datasets.

Papers

1. Main methods paper:
   1. Lawson, Hellenthal, Myers, and Falush (2012), "Inference of population structure using dense haplotype data", PLoS Genetics, 8 (e1002453). (preprint)
   2. Supporting Information in a single PDF file rather than many individual files), and some additional Supplementary material (the Whole World HGDP heatmap).
   3. See ChromoPainter and FineStructure (as well as the rest of the site) for more details.
2. Comparison paper to other linked methods:
   1. Lawson and Falush (2012), Similarity matrices and clustering algorithms for population identifcation using genetic data, Annual Review of Human Genomics, 13: 337-361. (preprint).
   2. Supplementary Material
   3. See Methods Comparison for more details.
3. What is a population?
   1. Lawson (2012), "What is a population? In statistical genetics modelling and inference", submitted book chapter for the interdisciplinary book "What is a Population", OUP. (preprint).
   2. See What Is A Population? for more details.

Information

1. Suitable Data sources for ChromoPainter (in construction).
2. Phasing advice for ChromoPainter.
3. A Complex example using our methods on large scale data.