ADMIXTOOLS

ADMIXTOOLS (or AdmixTools) is an R software package that is primarily used for analyzing admixture in population genetics. The initial version was originally developed by Nick Patterson and colleagues in 2012.[1] The second reimplemented version, ADMIXTOOLS 2, which has a revised point-and-click interface and improved speed, was developed jointly by Nick Patterson and David Reich.[2]

ADMIXTOOLS
Developer(s)Nick Patterson and David Reich
Initial release2012
Stable release
2.0
Repository
Written inR
Operating systemWindows, Linux, etc.
TypePopulation genetics
Websiteuqrmaie1.github.io/admixtools/

qpGraph

qpGraph is a software program that is part of the ADMIXTOOLS[3] software package developed by Patterson et al. (2012). qpGraph builds graphs that model genetic admixture in population relationships.[1] It estimates network topology likelihoods from a fixed number of admixture events,[4][5] based on the observed f-statistics.[6]

Other tools

Related statistical tools in the ADMIXTOOLS software package include qpAdm,[7] qpDstat, and qpWave.[8] qpDstat and qpWave test to see if populations form clades, while qpAdm estimates ancestry proportions.[2]

See also

References
  1. Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D (November 2012). "Ancient admixture in human history". Genetics. 192 (3): 1065–93. doi:10.1534/genetics.112.145037. PMC 3522152. PMID 22960212.
  2. "Inferring demographic history from genetic data". uqrmaie1.github.io. Retrieved 2022-05-18.
  3. "DReichLab/AdmixTools: Tools test whether admixture occurred and more". GitHub. Retrieved 2022-05-18.
  4. Molloy, Erin K; Durvasula, Arun; Sankararaman, Sriram (2021-07-01). "Advancing admixture graph estimation via maximum likelihood network orientation". Bioinformatics. Oxford University Press (OUP). 37 (Supplement_1): i142–i150. doi:10.1093/bioinformatics/btab267. ISSN 1367-4803. PMC 8336447. PMID 34252951.
  5. "Compute the fit of an admixture graph - qpgraph". uqrmaie1.github.io. Retrieved 2022-05-18.
  6. "Estimating Admixture Graphs with qpGraph". CompPopGenWorkshop2019 documentation. Retrieved 2022-05-18.
  7. Harney, Éadaoin; Patterson, Nick; Reich, David; Wakeley, John (2021-01-08). Novembre, J (ed.). "Assessing the performance of qpAdm: a statistical tool for studying population admixture". Genetics. Oxford University Press (OUP). 217 (4). doi:10.1093/genetics/iyaa045. ISSN 1943-2631.
  8. "Admixture modelling with qpWave and qpAdm". CompPopGenWorkshop2019 documentation. Retrieved 2022-05-18.


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