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MixMapper specifications


Unique identifier OMICS_13039
Name MixMapper
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data An array of SNP calls annotated with the population to which each individual belongs
Output data Predictions via bootstrap resampling
Operating system Unix/Linux
Programming languages C++, MATLAB
Computer skills Medium
Version 2.0
Stability Stable
Maintained Yes




No version available


  • person_outline Bonnie Berger

Publication for MixMapper

MixMapper citations


The genomic landscape of Nepalese Tibeto Burmans reveals new insights into the recent peopling of Southern Himalayas

Sci Rep
PMCID: 5686152
PMID: 29138459
DOI: 10.1038/s41598-017-15862-z
call_split See protocol

[…] es, by taking into account recent admixture involving SA and EA groups. For this purpose, we calculated a matrix of f2 statistics between each population pair by applying the procedure implemented in MIXMAPPER v2.0 and we used it to construct a neighbor-joining tree of non-admixed Asian populations selected according to f3 results. Supposed admixed populations were then fitted in the scaffold tree […]


Ancient European dog genomes reveal continuity since the Early Neolithic

Nat Commun
PMCID: 5520058
PMID: 28719574
DOI: 10.1038/ncomms16082

[…] were used to identify potential ancient dog–wolf admixture and f4-ratio tests to estimate dog–dog and dog–wolf admixture proportions were calculated using Admixtools. See and for more details. Both MixMapper and ADMIXTUREGRAPH were used to perform model-based inference of specific admixture events involving the three ancient dogs. MixMapper was performed on both the SNP array and whole-genome SN […]


Genomic Reconstruction of the History of Native Sheep Reveals the Peopling Patterns of Nomads and the Expansion of Early Pastoralism in East Asia

Mol Biol Evol
PMCID: 5850515
PMID: 28645168
DOI: 10.1093/molbev/msx181

[…] nd Z-score < −2 may indicate historical events of admixture ().Based on the results of the f3-statistic analysis, admixture events among Asian native sheep populations were further examined using the MixMapper v.2.0 program (, ). We first built the nonadmixed scaffold tree using the NJ method based on the pairwise f2-statistics () of 18 relatively nonadmixed populations (i.e., BGE, SUM, IDC, GUR, […]


Evolutionary Patterns and Processes: Lessons from Ancient DNA

Syst Biol
PMCID: 5410953
PMID: 28173586
DOI: 10.1093/sysbio/syw059

[…] dmixture graphs builds on the drift-based -statistics described above, generalizing a framework that has been efficiently implemented in several tools scalable up to a moderate number of populations. MixMapper, for example, implements a semi-automated method that first builds a neighbor-joining tree from the distances calculated between clearly non-admixed populations, and subsequently adds the r […]


The genetic history of Cochin Jews from India

Hum Genet
PMCID: 5020127
PMID: 27377974
DOI: 10.1007/s00439-016-1698-y

[…] timation α (i.e., it does not distinguish between α and 1-α), and therefore we used min(α,1-α) as a lower bound for the admixture proportion of the Jewish population in each significant pair. We used MixMapper (Lipson et al. ), with 100 bootstrap replicates, to calculate f2 values (Reich et al. ) that are needed to determine α from the output of ALDER two-reference test. We used Bonferroni correct […]


The Genetics of Bene Israel from India Reveals Both Substantial Jewish and Indian Ancestry

PLoS One
PMCID: 4806850
PMID: 27010569
DOI: 10.1371/journal.pone.0152056

[…] ficant pair. To determine α from the output of ALDER two-reference population test, f2 values (representing genetic drift between the two populations []) are needed [] and these were calculated using MixMapper [].(2) GLOBETROTTER: Given a putative admixed population and a set of populations (some of them may be a proxy for the presumed ancestral populations), GLOBETROTTER examines whether the puta […]


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MixMapper institution(s)
Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
MixMapper funding source(s)
This work was supported by the National Science Foundation Graduate Research Fellowship; HOMINID grant 1032255; and the National Institutes of Health grant GM100233.

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