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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.

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

qpGraph

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

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

Other tools

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

See also

• SplitsTree
• Dendroscope
• List of phylogenetics software

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. 12. 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. 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.

External links

• AdmixTools at GitHub
• AdmixTools 2 at GitHub
• qpGraph software package in Bioconductor 3.8. doi:10.18129/B9.bioc.qpgraph
• admixr – R package for reproducible analyses using ADMIXTOOLS

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