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Genetic ancestry estimation (DNA-seq analysis)

The estimation of genetic ancestry in human populations has important applications in medical genetic studies. Genetic ancestry is used to control for population stratification in genetic association studies, and is used to understand the genetic…
MIXSCORE
Desktop

MIXSCORE

Offers four statistical tests that have been used in studies of admixed…

Offers four statistical tests that have been used in studies of admixed populations. MIXSCORE is a method for combining single nucleotide polymorphism (SNP) association and admixture association…

LASER
Desktop
Web

LASER Locating Ancestry using SEquencing Reads

A program to estimate individual ancestry by directly analyzing shotgun…

A program to estimate individual ancestry by directly analyzing shotgun sequence reads without calling genotypes. LASER uses principal components analysis (PCA) and Procrustes analysis to analyze…

ADMIXTURE
Desktop

ADMIXTURE

A software tool for maximum likelihood estimation of individual ancestries from…

A software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.

ANCESTRYMAP
Desktop

ANCESTRYMAP

Finds skews in ancestry that are potentially associated with disease genes in…

Finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans.

SABER
Desktop

SABER

A program suitable for genome-scale data which uses a “Markov-hidden Markov…

A program suitable for genome-scale data which uses a “Markov-hidden Markov model” to estimate local ancestry.

frappe
Desktop

frappe

Estimates individual ancestry and admixture proportion. frappe is a full…

Estimates individual ancestry and admixture proportion. frappe is a full likelihood based estimator of individual admixture (IA) that uses high-density single nucleotide polymorphism (SNP) data.

bamova
Desktop

bamova

Implements a Bayesian Analysis of Molecular Variance and different likelihood…

Implements a Bayesian Analysis of Molecular Variance and different likelihood models for three different types of molecular data (including two models for high throughput sequence data). This model…

Ohana
Desktop

Ohana

Infers global ancestry, population covariances, and constructs population trees…

Infers global ancestry, population covariances, and constructs population trees using Gaussian models. The Ohana tool suite includes the following innovations: (i) An optimization method for…

HAPMIX
Desktop

HAPMIX

An application for accurately inferring chromosomal segments of distinct…

An application for accurately inferring chromosomal segments of distinct ancestry in admixed populations, using dense genetic data.

DIYABC
Desktop

DIYABC Do It Yourself ABC

A user-friendly approach to Approximate Bayesian Computation for inference on…

A user-friendly approach to Approximate Bayesian Computation for inference on population history using molecular markers.

ASAFE
Desktop

ASAFE Ancestry Specific Allele Frequency Estimation

Estimates ancestry-specific allele frequencies for bi-allelic markers. We…

Estimates ancestry-specific allele frequencies for bi-allelic markers. We derived an EM algorithm to estimate ancestry-specific allele frequencies given data on a 3-way admixed population. The major…

LAMP
Desktop

LAMP Local Ancestry in adMixed Populations

A software package for the inference of locus-specific ancestry in recently…

A software package for the inference of locus-specific ancestry in recently admixed populations.

sNMF
Desktop

sNMF

Estimates individual ancestry coefficients. sNMF is based on theoretical…

Estimates individual ancestry coefficients. sNMF is based on theoretical connections between likelihood approaches, principal component analysis (PCA), and nonnegative matrix factorization (NMF)…

admixturegraph
Desktop

admixturegraph

Explores and fits admixture graphs. admixturegraph allows to visualize goodness…

Explores and fits admixture graphs. admixturegraph allows to visualize goodness of fit and to evaluate the relative goodness of fit between different graphs. It can be used for brute-force search on…

NGSadmix
Desktop

NGSadmix

A method for inferring an individual's ancestry that takes the uncertainty…

A method for inferring an individual's ancestry that takes the uncertainty introduced in next generation sequencing data into account. This is achieved by working directly with genotype…

SNPWEIGHTS
Desktop

SNPWEIGHTS

A software package for inferring genome-wide genetic ancestry using SNP weights…

A software package for inferring genome-wide genetic ancestry using SNP weights precomputed from large external reference panels.

ObStruct
Desktop

ObStruct

A tool to objectively analyse the nature of structure revealed in Bayesian…

A tool to objectively analyse the nature of structure revealed in Bayesian ancestry profiles using established statistical methods.

GAGA
Dataset

GAGA Genetic Algorithm for Genetic Ancestry

A program developed to partition a distance matrix between pairs of objects…

A program developed to partition a distance matrix between pairs of objects into K clusters in order to minimize the amount of mean differences within each group (SSD'(WP) statistic).

LAIT
Desktop

LAIT Local Ancestry Inference Toolkit

Compiles several local ancestry inference softwares. LAIT allows users to…

Compiles several local ancestry inference softwares. LAIT allows users to preprocess, clean, and format PLINK files for being processed in four ancestry software packages (LAMP, LAMP-LD, HAPMIX,…

Popanc
Desktop

Popanc

A statistical method to estimate local ancestry frequencies in admixed…

A statistical method to estimate local ancestry frequencies in admixed populations when ongoing gene flow from source populations is rare or absent, but before genome stabilization is complete.…

Loter
Desktop

Loter

Allows users to perform haplotype phasing and local ancestry inference (LAI).…

Allows users to perform haplotype phasing and local ancestry inference (LAI). Loter is a python package that supplies a parameter-free and rapid software without specifications of statistical or…

fastNGSadmix
Desktop

fastNGSadmix

Allows users to calculate admixture proportions and perform principal component…

Allows users to calculate admixture proportions and perform principal component analysis (PCA) from next generation sequencing (NGS) data of a single individual. The analysis of fastNGSadmix is…

RFMix
Desktop

RFMix

A powerful discriminative modeling approach that is faster (~30x) and more…

A powerful discriminative modeling approach that is faster (~30x) and more accurate than existing methods. We accomplish this by using a conditional random field parameterized by random forests…

SEQMIX
Desktop

SEQMIX

Takes advantage of off-targeted sequence reads from exome/targeted sequencing…

Takes advantage of off-targeted sequence reads from exome/targeted sequencing experiments for accurate local ancestry inference. Before running SEQMIX, it is important to LD prune your data so that…

bammds
Desktop

bammds

A practical tool that allows visualization of samples sequenced by…

A practical tool that allows visualization of samples sequenced by second-generation sequencing when compared with a reference panel of individuals (usually genotypes) using a multidimensional…

iAdmix
Desktop

iAdmix

An efficient and versatile method for estimating the admixture proportions for…

An efficient and versatile method for estimating the admixture proportions for an individual's ancestry using genotype or sequence data and population allele frequencies from a set of…

POPBAM
Desktop

POPBAM

A comprehensive set of computational tools for evolutionary analysis of…

A comprehensive set of computational tools for evolutionary analysis of whole-genome alignments consisting of multiple individuals, from multiple populations or species. POPBAM works directly from…

Lanc-CSV
Desktop

Lanc-CSV

Uses continental-specific variants for accurate local ancestry inference.…

Uses continental-specific variants for accurate local ancestry inference. Lanc-CSV is an approach for local ancestry inference in fully sequenced recently admixed individuals. This method makes use…

AncestrySNPmine…
Web

AncestrySNPminer

Retrieves Ancestry Informative Markers (AIMs) from genomic data sets.…

Retrieves Ancestry Informative Markers (AIMs) from genomic data sets. AncestrySNPminer links these informative markers to genes and ontological annotation classes. It includes an automated and simple…

SimAdmix
Desktop

SimAdmix

Simulates chromosome admixture of various populations.

Simulates chromosome admixture of various populations.

GemTools
Desktop

GemTools

Provides computationally efficient tools for modeling genetic ancestry based in…

Provides computationally efficient tools for modeling genetic ancestry based in the SNP information.

ipPCA
Desktop

ipPCA iterative pruning Principal Component Analysis

Developed on the original ipPCA framework including additional functions that…

Developed on the original ipPCA framework including additional functions that result in improved population assignment accuracy.

MILANC error…
Desktop

MILANC error maps

Provides a lower bound on errors in the local ancestry estimates. MILANC is a…

Provides a lower bound on errors in the local ancestry estimates. MILANC is a method developed to observe in simulations underestimate the rate observed in real data and varies substantially across…

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