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]

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/

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]

See also

References
  1. 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. "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. doi:10.7554/eLife.85492. PMC 10310323. PMID 37057893.
  4. "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. Oxford University Press (OUP). 37 (Supplement_1): 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. Oxford University Press (OUP). 217 (4). doi:10.1093/genetics/iyaa045. ISSN 1943-2631. PMC 8049561.
  11. "Admixture modelling with qpWave and qpAdm". CompPopGenWorkshop2019 documentation. Retrieved 2022-05-18.


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