ADMIXTOOLS
Developer(s)Nick Patterson, Robert Maier, David Reich
Initial release2012
Repository
Written inC, C++, R
Operating systemWindows, Linux, etc.
TypePopulation genetics
Websiteuqrmaie1.github.io/admixtools/

ADMIXTOOLS (or AdmixTools) is a software package that is primarily used for analyzing admixture in population genetics. The original version was developed as a set of standalone C programs by Nick Patterson and colleagues and published in 2012.[1][2] A reimplemented version, ADMIXTOOLS 2, was developed as an R package by Robert Maier and colleagues and published in 2023.[3][4]

Most ADMIXTOOLS programs are based on fitting demographic models to f-statistics, which are calculated from population allele frequencies.[5]

qpGraph

qpGraph is a software program that is part of the ADMIXTOOLS[2] software package developed by Patterson et al. (2012). qpGraph evaluates graph-based models of population relationships with genetic admixture.[1] It estimates likelihoods of graphs with a fixed topology,[6][7] while adjusting graph parameters to fit observed f-statistics.[8]

ADMIXTOOLS 2 adds functionality for finding optimized graph topologies, similar to programs like Treemix.[9]

Other tools

Related statistical tools in the ADMIXTOOLS software package include qpAdm,[10] qpDstat, and qpWave.[11] qpDstat and qpWave test whether populations form clades, while qpAdm estimates ancestry proportions.[4] qpAdm is often used in conjunction with CP/NNLS.[12][13]

See also

References

  1. 1 2 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. 1 2 "DReichLab/AdmixTools: Tools test whether admixture occurred and more". GitHub. Retrieved 2022-05-18.
  3. ↑ Maier R, Flegontov P, Flegontova O, Işıldak U, Changmai P, Reich D (April 2023). "On the limits of fitting complex models of population history to f-statistics". eLife. 12. doi:10.7554/eLife.85492. PMC 10310323. PMID 37057893.
  4. 1 2 "Inferring demographic history from genetic data". uqrmaie1.github.io. Retrieved 2022-05-18.
  5. ↑ "f-statistics". Retrieved 2023-07-11.
  6. ↑ 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.
  7. ↑ "Compute the fit of an admixture graph - qpgraph". uqrmaie1.github.io. Retrieved 2022-05-18.
  8. ↑ "Estimating Admixture Graphs with qpGraph". CompPopGenWorkshop2019 documentation. Retrieved 2022-05-18.
  9. ↑ "Treemix". Retrieved 2023-07-11.
  10. ↑ 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): iyaa045. doi:10.1093/genetics/iyaa045. ISSN 1943-2631. PMC 8049561. PMID 33772284.
  11. ↑ "Admixture modelling with qpWave and qpAdm". CompPopGenWorkshop2019 documentation. Retrieved 2022-05-18.
  12. ↑ Järve, Mari; Saag, Lehti; Scheib, Christiana Lyn; Pathak, Ajai K.; Montinaro, Francesco; Pagani, Luca; Flores, Rodrigo; Guellil, Meriam; Saag, Lauri; Tambets, Kristiina; Kushniarevich, Alena; Solnik, Anu; Varul, Liivi; Zadnikov, Stanislav; Petrauskas, Oleg; Avramenko, Maryana; Magomedov, Boris; Didenko, Serghii; Toshev, Gennadi; Bruyako, Igor; Grechko, Denys; Okatenko, Vitalii; Gorbenko, Kyrylo; Smyrnov, Oleksandr; Heiko, Anatolii; Reida, Roman; Sapiehin, Serheii; Sirotin, Sergey; Tairov, Aleksandr; Beisenov, Arman; Starodubtsev, Maksim; Vasilev, Vitali; Nechvaloda, Alexei; Atabiev, Biyaslan; Litvinov, Sergey; Ekomasova, Natalia; Dzhaubermezov, Murat; Voroniatov, Sergey; Utevska, Olga; Shramko, Irina; Khusnutdinova, Elza; Metspalu, Mait; Savelev, Nikita; Kriiska, Aivar; Kivisild, Toomas; Villems, Richard (22 July 2019). "Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance". Current Biology. 29 (14): 2430–2441.e10. doi:10.1016/j.cub.2019.06.019. ISSN 0960-9822.
  13. ↑ Saag, Lehti; Vasilyev, Sergey V.; Varul, Liivi; Kosorukova, Natalia V.; Gerasimov, Dmitri V.; Oshibkina, Svetlana V.; Griffith, Samuel J.; Solnik, Anu; Saag, Lauri; D’Atanasio, Eugenia; Metspalu, Ene; Reidla, Maere; Rootsi, Siiri; Kivisild, Toomas; Scheib, Christiana Lyn; Tambets, Kristiina; Kriiska, Aivar; Metspalu, Mait (3 July 2020). "Genetic ancestry changes in Stone to Bronze Age transition in the East European plain". Science Advances. doi:10.1101/2020.07.02.184507. PMC 7817100.


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