ADMIXTOOLS

Last updated
ADMIXTOOLS
Developer(s) Nick Patterson, Robert Maier, David Reich
Initial release2012
Repository
Written in C, C++, R
Operating system Windows, 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]

Contents

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] and OrientAGraph. [10]

Other tools

Related statistical tools in the ADMIXTOOLS software package include qpAdm, [11] qpfst, qpF4ratio, qp3Pop, qpBound,qpDstat, andqpWave. [12] qpDstat and qpWave test whether populations form clades, while qpAdm estimates ancestry proportions. [4] qpAdm is often used in conjunction with CP/NNLS. [13] [14]

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. 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. ↑ Molloy, Erin K; Durvasula, Arun; Sankararaman, Sriram (4 August 2021). "Advancing admixture graph estimation via maximum likelihood network orientation". Bioinformatics. 37 (Supplement_1): i142 –i150. doi:10.1093/bioinformatics/btab267.
  11. ↑ 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.
  12. ↑ "Admixture modelling with qpWave and qpAdm". CompPopGenWorkshop2019 documentation. Retrieved 2022-05-18.
  13. ↑ 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. Bibcode:2019CBio...29E2430J. doi: 10.1016/j.cub.2019.06.019 . ISSN   0960-9822. PMID   31303491.
  14. ↑ 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). Bibcode:2021SciA....7.6535S. bioRxiv   10.1101/2020.07.02.184507 . doi:10.1126/sciadv.abd6535. ISSN   2375-2548. PMC   7817100 . PMID   33523926.
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