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ADMIXTOOLS
Developer(s) Nick Patterson, Robert Maier, David Reich
Initial release2012
Repository
Written in C, C++, R
Operating systemWindows, Linux, etc.
Type Population genetics
Website uqrmaie1.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. ^ a b 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. ^ a b "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. ^ a b "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. 37 (Supplement_1). Oxford University Press (OUP): 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. 217 (4). Oxford University Press (OUP): 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.

External links


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