ADMIXTOOLS explained

ADMIXTOOLS
Developer:Nick Patterson, Robert Maier, David Reich
Released:2012
Programming Language:C, C++, R
Engines:-->
Operating System:Windows, Linux, etc.
Genre:Population genetics
Licence:-->

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. A reimplemented version, ADMIXTOOLS 2, was developed as an R package by Robert Maier and colleagues and published in 2023.[1]

Most ADMIXTOOLS programs are based on fitting demographic models to f-statistics, which are calculated from population allele frequencies.[2]

qpGraph

qpGraph is a software program that is part of the ADMIXTOOLS[3] software package developed by Patterson et al. (2012). qpGraph evaluates graph-based models of population relationships with genetic admixture.[4] It estimates likelihoods of graphs with a fixed topology,[5] [6] while adjusting graph parameters to fit observed f-statistics.[7]

ADMIXTOOLS 2 adds functionality for finding optimized graph topologies, similar to programs like Treemix.[8]

Other tools

Related statistical tools in the ADMIXTOOLS software package include qpAdm,[9] qpfst, qpDstat, and qpWave.[10] qpDstat and qpWave test whether populations form clades, while qpAdm estimates ancestry proportions.[11] qpAdm is often used in conjunction with CP/NNLS.[12] [13]

See also

External links

Notes and References

  1. Maier R, Flegontov P, Flegontova O, Işıldak U, Changmai P, Reich D . On the limits of fitting complex models of population history to f-statistics . eLife . April 2023 . 12 . 37057893 . 10310323 . 10.7554/eLife.85492 . free .
  2. Web site: f-statistics . 2023-07-11.
  3. Web site: DReichLab/AdmixTools: Tools test whether admixture occurred and more . GitHub . 2022-05-18.
  4. Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D . Ancient admixture in human history . Genetics . 192 . 3 . 1065–93 . November 2012 . 22960212 . 3522152 . 10.1534/genetics.112.145037 .
  5. Molloy . Erin K . Durvasula . Arun . Sankararaman . Sriram . Advancing admixture graph estimation via maximum likelihood network orientation . Bioinformatics . Oxford University Press (OUP) . 37 . Supplement_1 . 2021-07-01 . 1367-4803 . 10.1093/bioinformatics/btab267 . i142–i150. 34252951 . 8336447 .
  6. Web site: Compute the fit of an admixture graph - qpgraph . uqrmaie1.github.io . . 2022-05-18.
  7. Web site: Estimating Admixture Graphs with qpGraph . CompPopGenWorkshop2019 documentation . . 2022-05-18.
  8. Web site: Treemix . 2023-07-11.
  9. Harney . Éadaoin . Patterson . Nick . Reich . David . Wakeley . John . Novembre . J . Assessing the performance of qpAdm: a statistical tool for studying population admixture . Genetics . Oxford University Press (OUP) . 217 . 4 . 2021-01-08 . iyaa045 . 1943-2631 . 10.1093/genetics/iyaa045. 33772284 . free . 8049561 .
  10. Web site: Admixture modelling with qpWave and qpAdm . CompPopGenWorkshop2019 documentation . . 2022-05-18.
  11. Web site: Inferring demographic history from genetic data . uqrmaie1.github.io . . 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 . 1. Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance . Current Biology . 22 July 2019 . 29 . 14 . 2430–2441.e10 . 10.1016/j.cub.2019.06.019 . 0960-9822. free .
  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 . 1. Genetic ancestry changes in Stone to Bronze Age transition in the East European plain . Science Advances . 7 . 4 . 2021-01-22 . 2375-2548 . 33523926 . 7817100 . 10.1126/sciadv.abd6535 . 10.1101/2020.07.02.184507.

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