1. ChromoPainter,
http://www.paintmychromosomes.com/
ChromoPainter is a tool for finding haplotypes in sequence data. Each individual is "painted" as a combination of all other sequences. 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
It is useful to generate high quality Principal Components Analysis (PCA) from dense data, for creating data summaries for fineSTRUCTURE, for dating admixture events, and much more.
2. 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.
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