Software:ADMIXTOOLS

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ADMIXTOOLS
Original author(s)
Developer(s)
Initial release2012
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] and OrientAGraph.[10]

Other tools

Related statistical tools in the ADMIXTOOLS software package include qpAdm,[11] qpfst, qpF4ratio, qp3Pop, qpBound, qpDstat, and qpWave.[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. ↑ 1.0 1.1 "Ancient admixture in human history". Genetics 192 (3): 1065–93. November 2012. doi:10.1534/genetics.112.145037. PMID 22960212. 
  2. ↑ 2.0 2.1 "DReichLab/AdmixTools: Tools test whether admixture occurred and more". https://github.com/DReichLab/AdmixTools. 
  3. ↑ "On the limits of fitting complex models of population history to f-statistics". eLife 12. April 2023. doi:10.7554/eLife.85492. PMID 37057893. 
  4. ↑ 4.0 4.1 "Inferring demographic history from genetic data". https://uqrmaie1.github.io/admixtools/index.html. 
  5. ↑ "f-statistics". https://uqrmaie1.github.io/admixtools/articles/fstats.html. 
  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. PMID 34252951. 
  7. ↑ "Compute the fit of an admixture graph - qpgraph". https://uqrmaie1.github.io/admixtools/reference/qpgraph.html. 
  8. ↑ "Estimating Admixture Graphs with qpGraph". https://comppopgenworkshop2019.readthedocs.io/en/latest/contents/07_qpgraph/qpGraph.html. 
  9. ↑ "Treemix". https://speciationgenomics.github.io/Treemix/. 
  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 (Oxford University Press (OUP)) 217 (4). doi:10.1093/genetics/iyaa045. ISSN 1943-2631. PMID 33772284. 
  12. ↑ "Admixture modelling with qpWave and qpAdm". https://comppopgenworkshop2019.readthedocs.io/en/latest/contents/05_qpwave_qpadm/qpwave_qpadm.html. 
  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. doi:10.1016/j.cub.2019.06.019. ISSN 0960-9822. PMID 31303491. Bibcode: 2019CBio...29E2430J. 
  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). doi:10.1126/sciadv.abd6535. ISSN 2375-2548. PMID 33523926. Bibcode: 2021SciA....7.6535S. 



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