Software available at this site
FineSTRUCTURE version 2, a pipeline
for running ChromoPainter and FineSTRUCTURE for population
inference. A GUI is available for interpretation. Download from the Downloads
page.
FineSTRUCTURE R scripts, a facility for
exploring the results when the GUI is unavailable.
GLOBETROTTER, the admixture dating method
based on ChromoPainter. Download from the Downloads
page.
badMIXTURE, An R package to
inmterpret the results of ADMIXTURE and STRUCTURE-like mixture models.
RADpainter, finestructure and ChromoPainter
for RAD tag data used for non-model organisms.
Scripts to perform many types of conversion. Included in the main
software download from the Downloads
page.
What this page is
This page provides information about and downloads for
methodology for
Chromosome Painting. It is not a facility to analyse your genome. Sorry if
you were misled by the punchy name!
About 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.
The included ChromoPainter tool finds `haplotypes' in sequence data.
Each individual is "painted" as a combination of all other sequences.
ChromoPainter 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 clustering individuals with FineSTRUCTURE,
for dating admixture events, and much more.
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.