:: DESCRIPTION
SpaceMix is a method for inferring and visualizing spatial patterns of population genetic structure and admixture.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bradburd GS, Ralph PL, Coop GM.
A Spatial Framework for Understanding Population Structure and Admixture.
PLoS Genet. 2016 Jan 15;12(1):e1005703. doi: 10.1371/journal.pgen.1005703. PMID: 26771578; PMCID: PMC4714911.
:: DESCRIPTION
The POPS program performs inference of ancestry distribution models. It uses a TESS-like interface to compute individual cluster membership and admixture proportions based on multilocus genotype data and their correlation with environmental and geographical variables.
::DEVELOPER
the Computational and Mathematical Biology group in Grenoble
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
F. Jay, O. François, M. Blum (2011)
Predictions of Native American Population Structure Using Linguistic Covariates in a Hidden Regression Framework.
PLoS ONE 6(1): e16227
:: DESCRIPTION
AdmixKJump detects the number of populations in a cohort of samples with smaller sample sizes and shorter divergence times.
::DEVELOPER
O’Connor Evolutionary Genomics Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
AdmixKJump: identifying population structure in recently diverged groups.
O’Connor TD.
Source Code Biol Med. 2015 Feb 3;10(1):2. doi: 10.1186/s13029-014-0031-1.
:: DESCRIPTION
SHIPS is a non-parametric clustering algorithm that clusters individuals from a population into genetically homogeneous sub-populations from genotype data.
::DEVELOPER
Matthieu Bouaziz <matthieu.x.bouaziz@gmail.com>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2012;7(10):e45685. doi: 10.1371/journal.pone.0045685. Epub 2012 Oct 12.
SHIPS: Spectral Hierarchical clustering for the Inference of Population Structure in genetic studies.
Bouaziz M, Paccard C, Guedj M, Ambroise C.
:: DESCRIPTION
sNMF (Sparse Non-negative Matrix Factorization) is a fast and efficient method for the inference of Admixture Coefficients.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genetics. 2014 Apr;196(4):973-83. doi: 10.1534/genetics.113.160572. Epub 2014 Feb 4.
Fast and efficient estimation of individual ancestry coefficients.
Frichot E1, Mathieu F, Trouillon T, Bouchard G, François O.
:: DESCRIPTION
fastStructure is an algorithm for inferring population structure from large SNP genotype data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
fastSTRUCTURE: variational inference of population structure in large SNP data sets.
Raj A, Stephens M, Pritchard JK.
Genetics. 2014 Jun;197(2):573-89. doi: 10.1534/genetics.114.164350
:: DESCRIPTION
Structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Daniel Falush, Matthew Stephens, and Jonathan K. Pritchard
Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies
Genetics, Vol. 164, 1567-1587,
:: DESCRIPTION
distruct is a program that can be used to graphically display results produced by the genetic clustering program structure or by other similar programs.
::DEVELOPER
Rosenberg lab at Stanford University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Noah A. Rosenberg
DISTRUCT: a program for the graphical display of population structure
Molecular Ecology Notes (2004) 4, 137–138
:: DESCRIPTION
The popkin (population kinship) R package estimates the kinship matrix of individuals and FST from their biallelic genotypes. Our estimation framework is the first to be practically unbiased under arbitrary population structures.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ochoa, Alejandro, and John D. Storey. 2016b.
“FST And Kinship for Arbitrary Population Structures II: Method of Moments Estimators.”
bioRxiv doi:10.1101/083923.
:: DESCRIPTION
LMM-Lasso is a linear mixed models that allows for both multi-locus mapping and correction for confounding effects.
::DEVELOPER
Machine Learning and Computational Biology Research Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Jan 15;29(2):206-14. doi: 10.1093/bioinformatics/bts669.
A Lasso multi-marker mixed model for association mapping with population structure correction.
Rakitsch B, Lippert C, Stegle O, Borgwardt K.
