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ADMIXTOOLS

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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

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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

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Related statistical tools in the ADMIXTOOLS software package include qpAdm,[10] qpfst, qpF4ratio, qp3Pop, qpBound, 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

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References

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  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; et al. (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; et al. (2021-01-22). "Genetic ancestry changes in Stone to Bronze Age transition in the East European plain". Science Advances. 7 (4). bioRxiv 10.1101/2020.07.02.184507. doi:10.1126/sciadv.abd6535. ISSN 2375-2548. PMC 7817100. PMID 33523926.
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