Chromopainterv2

Chromopainterv2 is a piece of software which can be used to infer patterns of haplotype sharing between individuals/populations. This information can be used to, amongst other things, infer population structure (fineSTRUCTURE), date admixture events (GLOBETROTTER) and estimate admixture proportions (SOURCEFIND). The original paper which describes the technical details can be found here here, and the source code, examples and instructions can be downloaded here:

https://github.com/sahwa/ChromoPainterv2

Plot of haplotype-sharing differences between two ancient individuals from Broushaki et al (2016)

SOURCEFIND

SOURCEFIND is an R package which can be used to infer copying proportions from the output of ChromoPainter and can be downloaded from:

https://github.com/sahwa/sourcefindV2

The technical description of the algorithm can be found in the supplementary methods of Latin Americans show wide-spread Converso ancestry and imprint of local Native ancestry on physical appearance.

Sourcefind copying proportions from Chacon-Duque et al (2019)

GLOBETROTTER

GLOBETROTTER is piece of software which is able to infer and date admixture events, in addition to estimating admixture proportions from ChromoPainter output and can be downloaded from:

https://github.com/sahwa/GLOBETROTTER

The technical description of the algorithm can be found in the supplementary methods of A genetic atlas of human admixture history.

An interactive exploration of GLOBETROTTER applied to worldwide modern populations can be found here.

Co-ancestry curves for simulated admixed individuals

fastGLOBETROTTER

fastGLOBETROTTER is a new version of the same model, using the same input, that is ~4-20 times faster than GLOBETROTTER without sacrificing accuracy. The paper published in Genome Research can be found here.

https://github.com/sahwa/fastGLOBETROTTER

AdaptMix

AdaptMix is a program designed to detect evidence of selection at genome-wide SNPs in admixed populations and determine whether selection occurred before or after admixture, as well as inferring selection coefficients. The methodology has been described in a paper in Molecular Biology and Evolution, Disentangling Signatures of Selection Before and After European Colonization in Latin Americans.