ADMIXTOOLS

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ADMIXTOOLS
Developer(s)Nick Patterson, Robert Maier, David Reich
Initial release2012
Repository
Written in
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]

Other tools

Related statistical tools in the ADMIXTOOLS software package include qpAdm,

qpAdm is often used in conjunction with CP/NNLS.[12][13]

See also

References

  1. ^
    PMID 22960212
    .
  2. ^ a b "DReichLab/AdmixTools: Tools test whether admixture occurred and more". GitHub. Retrieved 2022-05-18.
  3. PMID 37057893
    .
  4. ^ a b "Inferring demographic history from genetic data". uqrmaie1.github.io. Retrieved 2022-05-18.
  5. ^ "f-statistics". Retrieved 2023-07-11.
  6. 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. PMID 33772284
    .
  11. ^ "Admixture modelling with qpWave and qpAdm". CompPopGenWorkshop2019 documentation. Retrieved 2022-05-18.
  12. ISSN 0960-9822
    .
  13. PMID 33523926
    .

External links


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