ADMIXMAP

ADMIXMAP is a software tool to estimate admixture and detects linkage in admixed populations. The ADMIXMAP algorithm uses Bayesian inference

Population genetics;Genotype and phenotype

Operation: Modelling and simulation
Software interface: Command-line user interface
Language: C++
License: -
Cost: Free
Version name: 3.7
Credit: National Institutes of Health (NIH).
Input: genotypesfile, testgenotypesfile,allelefreqfile, priorallelefreqfile, historicallelefreqfile, outcomevarfile, covariatesfile,coxoutcomevarfile
Output: paramfile, regparamfile, dispparamfile, indadmixturefile, allelefreqoutputfile, ergodicaveragefile, admixturescorefile, allelicassociationscorefile, ancestryassociationscorefile, affectedsonlyscorefile, args.txt
Contact: Paul M McKeigue paul.mckeigue at ucd.ie
Collection: -
Maturity: -

Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations.
McKeigue PM, Carpenter JR, Parra EJ, Shriver MD (2000). Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations. Ann Hum Genet 64(Pt 2): 171-86.
https://doi.org/10.1017/S0003480000008022
PMID: 11246470
PMC: -

Control of confounding of genetic associations in stratified populations.
Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, et al. (2003). Control of confounding of genetic associations in stratified populations. Am J Hum Genet 72(6): 1492-1504.
https://doi.org/10.1086/375613
PMID: 12817591
PMC: PMC1180309

Design and analysis of admixture mapping studies.
Hoggart CJ, Shriver MD, Kittles RA, Clayton DG, McKeigue PM. Design and analysis of admixture mapping studies. Am J Hum Genet. 2004 May;74(5):965-78. doi: 10.1086/420855. Epub 2004 Apr 14. PMID: 15088268; PMCID: PMC1181989.
https://doi.org/10.1086/420855
PMID: 15088268
PMC: PMC1181989

Prospects for admixture mapping of complex traits.
McKeigue PM (2005). Prospects for admixture mapping of complex traits. Am J Hum Genet 76(1): 1-7.
https://doi.org/10.1086/426949
PMID: 15540159
PMC: PMC1196412

Source: https://sourceforge.net/projects/admixmap/files/admixmap/
Documentation: http://admixmap.sourceforge.net/manual_main.html
Home page: http://www.homepages.ed.ac.uk/pmckeigu/admixmap/index.html
Links: http://admixmap.sourceforge.net/admixmap_tutorial.html
Links: http://admixmap.sourceforge.net/admixmap_install.html
Links: https://precmed.cphs.mvm.ed.ac.uk/pmckeigue/software/admixmap/manual_desc.html