{{Short description|Population genetics software package}} {{Infobox software | title = ADMIXTOOLS | name = | logo = | logo caption = | logo alt = | logo size = | screenshot = | screenshot size = | screenshot alt = | caption = | other_names = | author = {{UBL| Nick Patterson | David Reich }} | developer = {{UBL| Robert Maier | David Reich Lab }} | released = 2012 | ver layout = | discontinued = | latest release date = | latest preview version = | latest preview date = | repo = | qid = | programming language = C, C++, R | middleware = | engine = | operating system = Windows, Linux, etc. | platform = | included with = | replaces = | replaced_by = | service_name = | size = | standard = | language = | language count = | language footnote = | genre = Population genetics | license = | website = {{URL|https://uqrmaie1.github.io/admixtools/}} | AsOf = }}
'''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.<ref name="Patterson 2012"/><ref name="Patterson GH"/> A reimplemented version, ADMIXTOOLS 2, was developed as an R package by Robert Maier and colleagues and published in 2023.<ref name="Maier 2023">{{cite journal |vauthors=Maier R, Flegontov P, Flegontova O, Işıldak U, Changmai P, Reich D |title=On the limits of fitting complex models of population history to f-statistics |journal=eLife |date=April 2023 |volume=12 |pmid=37057893 |pmc=10310323 |doi=10.7554/eLife.85492 |doi-access=free }}</ref><ref name="auto"/>
Most ADMIXTOOLS programs are based on fitting demographic models to f-statistics, which are calculated from population allele frequencies.<ref>{{cite web |title=f-statistics |url=https://uqrmaie1.github.io/admixtools/articles/fstats.html |access-date=2023-07-11}}</ref>
==qpGraph== '''qpGraph''' is a software program that is part of the ADMIXTOOLS<ref name="Patterson GH">{{cite web |title=DReichLab/AdmixTools: Tools test whether admixture occurred and more |website=GitHub |url=https://github.com/DReichLab/AdmixTools |access-date=2022-05-18}}</ref> software package developed by Patterson et al. (2012). qpGraph evaluates graph-based models of population relationships with genetic admixture.<ref name="Patterson 2012">{{cite journal |vauthors=Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D |title=Ancient admixture in human history |journal=Genetics |volume=192 |issue=3 |pages=1065–93 |date=November 2012 |pmid=22960212 |pmc=3522152 |doi=10.1534/genetics.112.145037 }}</ref> It estimates likelihoods of graphs with a fixed topology,<ref>{{cite journal |last1=Molloy |first1=Erin K |last2=Durvasula |first2=Arun |last3=Sankararaman |first3=Sriram |title=Advancing admixture graph estimation via maximum likelihood network orientation |journal=Bioinformatics |publisher=Oxford University Press (OUP) |volume=37 |issue=Supplement_1 |date=2021-07-01 |issn=1367-4803 |doi=10.1093/bioinformatics/btab267 |pages=i142–i150|pmid=34252951 |pmc=8336447 }}</ref><ref>{{cite web |title=Compute the fit of an admixture graph - qpgraph |website=uqrmaie1.github.io |url=https://uqrmaie1.github.io/admixtools/reference/qpgraph.html |ref={{sfnref |uqrmaie1.github.io}} |access-date=2022-05-18}}</ref> while adjusting graph parameters to fit observed f-statistics.<ref>{{cite web |title=Estimating Admixture Graphs with qpGraph |website=CompPopGenWorkshop2019 documentation |url=https://comppopgenworkshop2019.readthedocs.io/en/latest/contents/07_qpgraph/qpGraph.html |ref={{sfnref |CompPopGenWorkshop2019 documentation}} |access-date=2022-05-18}}</ref>
ADMIXTOOLS 2 adds functionality for finding optimized graph topologies, similar to programs like Treemix<ref>{{cite web |title=Treemix |url=https://speciationgenomics.github.io/Treemix/ |access-date=2023-07-11}}</ref> and OrientAGraph.<ref>{{cite journal |last1=Molloy |first1=Erin K |last2=Durvasula |first2=Arun |last3=Sankararaman |first3=Sriram |title=Advancing admixture graph estimation via maximum likelihood network orientation |journal=Bioinformatics |date=4 August 2021 |volume=37 |issue=Supplement_1 |pages=i142–i150 |doi=10.1093/bioinformatics/btab267|pmc=8336447 }}</ref>
==Other tools== Related statistical tools in the ADMIXTOOLS software package include '''qpAdm,<ref>{{cite journal |last1=Harney |first1=Éadaoin |last2=Patterson |first2=Nick |last3=Reich |first3=David |last4=Wakeley |first4=John |editor-last=Novembre |editor-first=J |title=Assessing the performance of qpAdm: a statistical tool for studying population admixture |journal=Genetics |publisher=Oxford University Press (OUP) |volume=217 |issue=4 |date=2021-01-08 |article-number=iyaa045 |issn=1943-2631 |doi=10.1093/genetics/iyaa045|pmid=33772284 |doi-access=free |pmc=8049561 }}</ref>''' '''qpfst, qpF4ratio, qp3Pop, qpBound,''' '''qpDstat, and''' '''qpWave.<ref>{{cite web |title=Admixture modelling with qpWave and qpAdm |website=CompPopGenWorkshop2019 documentation |url=https://comppopgenworkshop2019.readthedocs.io/en/latest/contents/05_qpwave_qpadm/qpwave_qpadm.html |ref={{sfnref |CompPopGenWorkshop2019 documentation}} |access-date=2022-05-18}}</ref>''' qpDstat and qpWave test whether populations form clades, while qpAdm estimates ancestry proportions.<ref name="auto">{{cite web |title=Inferring demographic history from genetic data |website=uqrmaie1.github.io |url=https://uqrmaie1.github.io/admixtools/index.html |ref={{sfnref |uqrmaie1.github.io}} |access-date=2022-05-18}}</ref> qpAdm is often used in conjunction with CP/NNLS.<ref>{{cite journal |last1=Järve |first1=Mari |last2=Saag |first2=Lehti |last3=Scheib |first3=Christiana Lyn |last4=Pathak |first4=Ajai K. |last5=Montinaro |first5=Francesco |last6=Pagani |first6=Luca |last7=Flores |first7=Rodrigo |last8=Guellil |first8=Meriam |last9=Saag |first9=Lauri |last10=Tambets |first10=Kristiina |last11=Kushniarevich |first11=Alena |last12=Solnik |first12=Anu |last13=Varul |first13=Liivi |last14=Zadnikov |first14=Stanislav |last15=Petrauskas |first15=Oleg |last16=Avramenko |first16=Maryana |last17=Magomedov |first17=Boris |last18=Didenko |first18=Serghii |last19=Toshev |first19=Gennadi |last20=Bruyako |first20=Igor |last21=Grechko |first21=Denys |last22=Okatenko |first22=Vitalii |last23=Gorbenko |first23=Kyrylo |last24=Smyrnov |first24=Oleksandr |last25=Heiko |first25=Anatolii |last26=Reida |first26=Roman |last27=Sapiehin |first27=Serheii |last28=Sirotin |first28=Sergey |last29=Tairov |first29=Aleksandr |last30=Beisenov |first30=Arman |last31=Starodubtsev |first31=Maksim |last32=Vasilev |first32=Vitali |last33=Nechvaloda |first33=Alexei |last34=Atabiev |first34=Biyaslan |last35=Litvinov |first35=Sergey |last36=Ekomasova |first36=Natalia |last37=Dzhaubermezov |first37=Murat |last38=Voroniatov |first38=Sergey |last39=Utevska |first39=Olga |last40=Shramko |first40=Irina |last41=Khusnutdinova |first41=Elza |last42=Metspalu |first42=Mait |last43=Savelev |first43=Nikita |last44=Kriiska |first44=Aivar |last45=Kivisild |first45=Toomas |last46=Villems |first46=Richard |display-authors=1|title=Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance |journal=Current Biology |date=22 July 2019 |volume=29 |issue=14 |pages=2430–2441.e10 |doi=10.1016/j.cub.2019.06.019 |issn=0960-9822|doi-access=free |pmid=31303491 |bibcode=2019CBio...29E2430J }}</ref><ref>{{cite journal | last1=Saag | first1=Lehti | last2=Vasilyev | first2=Sergey V. | last3=Varul | first3=Liivi | last4=Kosorukova | first4=Natalia V. | last5=Gerasimov | first5=Dmitri V. | last6=Oshibkina | first6=Svetlana V. | last7=Griffith | first7=Samuel J. | last8=Solnik | first8=Anu | last9=Saag | first9=Lauri | last10=D'Atanasio | first10=Eugenia | last11=Metspalu | first11=Ene | last12=Reidla | first12=Maere | last13=Rootsi | first13=Siiri | last14=Kivisild | first14=Toomas | last15=Scheib | first15=Christiana Lyn | last16=Tambets | first16=Kristiina | last17=Kriiska | first17=Aivar | last18=Metspalu | first18=Mait |display-authors=1| title=Genetic ancestry changes in Stone to Bronze Age transition in the East European plain | journal=Science Advances | volume=7 | issue=4 | date=2021-01-22 | issn=2375-2548 | pmid=33523926 | pmc=7817100 | doi=10.1126/sciadv.abd6535 | bibcode=2021SciA....7.6535S |biorxiv=10.1101/2020.07.02.184507 }}</ref>
==See also== *SplitsTree *Dendroscope *List of phylogenetics software
==References== {{Reflist}}
==External links== *[https://github.com/DReichLab/AdmixTools AdmixTools] at GitHub *[https://github.com/uqrmaie1/admixtools AdmixTools 2] at GitHub *[https://bioconductor.riken.jp/packages/3.8/bioc/html/qpgraph.html qpGraph software package] in Bioconductor 3.8. {{doi|10.18129/B9.bioc.qpgraph}} *[http://hdl.handle.net/21.11116/0000-0002-D219-5 admixr] – R package for reproducible analyses using ADMIXTOOLS
Category:Phylogenetics software Category:Free R (programming language) software