|
Critical Commercial Assays
|
| Infinium Multi-Ethnic Global-8 Kit |
Illumina |
WG-316 |
|
Deposited Data
|
| Genetic data from Bayira (Mota) |
12
|
DOI: 10.1126/science.aad2879
|
| Genetic data from Sandawe and Hadza people |
22
|
DOI: 10.1073/pnas.1017511108
|
| Genetic data from Bari, Bataheen, Beni-Amer, Beri, Copts, Danagla, Dinka, Gemar, Hadendowa, Halfawieen, Hausa, Ja'alin, Mahas, Misseriya, Nuba, Nuer, Shaigiya, and Shilluk people |
52
|
DOI: 10.1371/journal.pgen.1006976
|
| Genetic data from Mbuti people |
57
|
DOI: 10.1038/nature18964
|
| Genetic data from Aari Blacksmith, Aari Cultivator, Afar, Anuak, Tigray, Amhara, Ethiopian Somali, Gumuz, Oromo, and Wolayta people |
52
|
DOI: 10.1016/j.ajhg.2012.05.015
|
| Genetic data from Amhara, Egyptian, Ethiopian Somali, Gumuz, Oromo, and Wolayta people |
53
|
DOI: 10.1016/j.ajhg.2015.04.019
|
| Genetic data from Bakiga and Batwa people |
55
|
DOI: 10.1073/pnas.1402875111
|
| Genetic data from ancient African individuals |
Allen Ancient DNA Resource (v. 44.3) |
https://reich.hms.harvard.edu/allen-ancient-dna-resource-aadr-downloadable-genotypes-present-day-and-ancient-dna-data
|
| Genetic data from Bench, Chabu, Majang, Shekkacho, and Sheko people |
This study, deposited on dbGaP |
phs001123.v2.p2 |
|
Software and Algorithms
|
| Custom scripts |
This study, deposited on Zenodo |
DOI: 10.5281/zenodo.5911732
|
| ADMIXTOOLS |
18
|
https://github.com/DReichLab/AdmixTools
|
| ADMIXTURE |
14
|
https://dalexander.github.io/admixture/download.html
|
| ALDER |
17
|
https://github.com/joepickrell/malder/tree/master/MALDER
|
| a-LoCoH, implemented in adehabitatHR (R package) |
74
|
https://cran.r-project.org/web/packages/adehabitatHR/index.html
|
| EEMS |
19
|
https://github.com/dipetkov/eems
|
| GARLIC |
76
|
https://github.com/szpiech/garlic
|
| GenomeStudio v2.0.3 |
NA |
https://support.illumina.com/array/array_software/genomestudio/downloads.html
|
| hap-ibd v1.0 |
79
|
https://github.com/browning-lab/hap-ibd
|
| IBDNe (ibdne.04Sep15.e78) |
23
|
https://faculty.washington.edu/browning/ibdne.html
|
| maptools (R package) |
The Comprehensive R Archive Network |
https://cran.r-project.org/web/packages/maptools/index.html
|
| msprime |
24
|
https://github.com/tskit-dev/msprime
|
| PLINK 1.9 |
60
|
https://www.cog-genomics.org/plink/
|
| PONDEROSA |
58
|
https://github.com/williamscole/PONDEROSA
|
| R |
The R Project for Statistical Computing |
https://www.r-project.org/
|
| RColorBrewer (R package) |
The Comprehensive R Archive Network |
https://cran.r-project.org/web/packages/RColorBrewer/index.html
|
| SHAPEIT2 |
78
|
https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html
|
| smartpca |
64
|
https://github.com/DReichLab/EIG
|
| Spatial ancestry plotting functions |
Ryan Raaum 53
|
DOI: 10.1534/genetics.116.187369
|
| vegan (R package) |
The Comprehensive R Archive Network |
https://cran.r-project.org/web/packages/vegan/index.html
|
| zCall |
50
|
https://github.com/jigold/zCall
|
