Chromosome Painting
Painting is an efficient way of identifying important haplotype information from dense genotype data. It describes ancestry in an efficient way suitable for a range of further analyses, including population identification and admixture dating.
About ChromoPainter
ChromoPainter is a tool for finding haplotypes in sequence data. Each individual is "painted" as a combination of all other sequences. (See the ChromoPainter page for an description of how this works.)It can output a range of features, including:
- Sample haplotypes
- Expectations of the number of recombination events at all sites
- A wide range of related features
Because it is highly parallelizable, ChromoPainter can produce a lot of files on a lot of machines. To help you combine them correctly, we have created a tool called ChromoCombine.
About fineSTRUCTURE
fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data. By using the output of ChromoPainter as a (nearly) sufficient summary statistic, it is able to perform model-based Bayesian clustering on large datasets, including full resequencing data, and can handle up to 1000s of individuals. Full assignment uncertainty is given.