Software:ADMIXTOOLS
| Developer(s) | Nick Patterson, Robert Maier, David Reich |
|---|---|
| Initial release | 2012 |
| Written in | C, C++, R |
| Operating system | Windows, Linux, etc. |
| Type | Population genetics |
| Website | uqrmaie1 |
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]
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] qpAdm is often used in conjunction with CP/NNLS.[12][13]
See also
References
- ↑ 1.0 1.1 "Ancient admixture in human history". Genetics 192 (3): 1065–93. November 2012. doi:10.1534/genetics.112.145037. PMID 22960212.
- ↑ 2.0 2.1 "DReichLab/AdmixTools: Tools test whether admixture occurred and more". https://github.com/DReichLab/AdmixTools.
- ↑ "On the limits of fitting complex models of population history to f-statistics". eLife 12. April 2023. doi:10.7554/eLife.85492. PMID 37057893.
- ↑ 4.0 4.1 "Inferring demographic history from genetic data". https://uqrmaie1.github.io/admixtools/index.html.
- ↑ "f-statistics". https://uqrmaie1.github.io/admixtools/articles/fstats.html.
- ↑ 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.
- ↑ "Compute the fit of an admixture graph - qpgraph". https://uqrmaie1.github.io/admixtools/reference/qpgraph.html.
- ↑ "Estimating Admixture Graphs with qpGraph". https://comppopgenworkshop2019.readthedocs.io/en/latest/contents/07_qpgraph/qpGraph.html.
- ↑ "Treemix". https://speciationgenomics.github.io/Treemix/.
- ↑ 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): iyaa045. doi:10.1093/genetics/iyaa045. ISSN 1943-2631. PMID 33772284.
- ↑ "Admixture modelling with qpWave and qpAdm". https://comppopgenworkshop2019.readthedocs.io/en/latest/contents/05_qpwave_qpadm/qpwave_qpadm.html.
- ↑ Järve, Mari; Saag, Lehti; Scheib, Christiana Lyn; Pathak, Ajai K.; Montinaro, Francesco; Pagani, Luca; Flores, Rodrigo; Guellil, Meriam 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. https://www.sciencedirect.com/science/article/pii/S0960982219307122.
- ↑ Saag, Lehti; Vasilyev, Sergey V.; Varul, Liivi; Kosorukova, Natalia V.; Gerasimov, Dmitri V.; Oshibkina, Svetlana V.; Griffith, Samuel J.; Solnik, Anu et al. (3 July 2020). "Genetic ancestry changes in Stone to Bronze Age transition in the East European plain". Science Advances. doi:10.1101/2020.07.02.184507. PMC 7817100. https://www.science.org/doi/10.1126/sciadv.abd6535.
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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