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 statistics to increase power in genome-wide association study (GWAS) in admixed populations. The MIXSCORE approach requires local-ancestry estimates as input, which can be estimated by any method.
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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 sequence reads of each sample and place the sample into a reference PCA space constructed using genotypes of a set of reference individuals. With an appropriate reference panel, the estimated coordinates of the sequence samples reflect their ancestral background and can be used to correct for population stratification in association studies. LASER can accurately estimate ancestry even with modest amounts of data, such as the off-target sequence data generated by targeted sequencing experiments. LASER can be used to improve case-control matching in genetic association studies and to reduce the risk of spurious findings due to population structure.
A software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.
Investigates single nucleotide polymorphism (SNP) data. DIYABC is based on a simulation algorithm allowing the treatment of multi-population datasets with large number of loci. It can take into account complex population histories including any combination of population divergence events, admixture events and changes in past population size. This tool can serve to compare competing evolutionary scenarios and quantify their relative support.
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 will facilitate the population genetic analysis of a wide range of organisms on the basis of next-generation sequence data.
Finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans.
A program suitable for genome-scale data which uses a “Markov-hidden Markov model” to estimate local ancestry.
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 trained on reference panels. RFMix is capable of learning from the admixed samples themselves to boost performance and autocorrect phasing errors. RFMix shows high sensitivity and specificity in simulated Hispanics/Latinos and African Americans and admixed Europeans, Africans, and Asians.
Intends to estimate relatedness in samples from structured populations with admixed ancestry. REAP measures autosomal kinship coefficients and identity-by-descent (IBD) sharing probabilities from single nucleotide polymorphism (SNP) genotype data. The application integrates functionalities allowing users to specify a subset of individuals to include in the relatedness estimation analysis as well as an inbreeding-coefficient estimator.
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 pairs of sites in high LD (r^2 > 0.1) are identified and only the one with a higher sequence depth are included into the model. As the sequence depth distribution is sample dependent, it is necessary to prune the sequence data for each individual.
A software package for the inference of locus-specific ancestry in recently admixed populations.
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 scaling algorithm.
A software package for inferring genome-wide genetic ancestry using SNP weights precomputed from large external reference panels.
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 the genome. The MILANC rate provides a real data-based evaluation of local ancestry estimates as opposed to simulations that cannot measure systematic inaccuracies arising from violations of model assumptions.
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 the graph topologies or for a heuristic approach generalizing the sequential one. It allows to make genetic lineages. The tool provides functionality for exploring the space of possible topologies. It computes Bayes factors between graphs for comparing them.
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 advantage of ASAFE over alternative ancestry-specific allele frequency estimation approaches is that ASAFE is applicable to markers in the admixed sample that are absent from a reference panel. Furthermore, ASAFE takes advantage of linkage-disequilibrium based information by using local ancestry calls.
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 rested on a set of predefined reference populations and genotype likelihoods of the input sample. This method corrects the biases introduced by small reference populations, and is useful including for low sequencing depth.
Assists users for visualizing ancestry data. AncestryView first proceeds by reading the command line parameters and generating a color scheme. It then extracts the sample IDs and uptakes the digital ancestral data from ancestry of modern admixed populations (aMAP) data or other ancestry inference software. A genome or chromosome map of local ancestry is produced, as well as some legends and statistics of the aMAP results.
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 STRUCTURE-style modeling for inferring admixture in a maximum likelihood estimate (MLE) framework. This method is applicable both to called genotypes and to next generation sequencing (NGS) data with uncertainty regarding the true genotypes. The method solves the sequential quadratic programming (QP) problem based on the Active Set algorithm, and tends to find higher maximum likelihood values than ADMIXTURE in similar computational time. (ii) A method for estimating population relationships from ancestry components using a Gaussian approximation. Ohana estimates the best covariance matrix compatible with a tree, thereby estimating a tree, and provides simple algorithms and visualization tools to obtain the evolutionary trees.
An application for accurately inferring chromosomal segments of distinct ancestry in admixed populations, using dense genetic data.
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Estimating genetic kin relationships in prehistoric populations
Tools (3):
PLINK, REAP, GRAB
Topics (2):
WGS analysis, Homo sapiens
Exome Sequencing Identifies Genetic Variants Associated with Circulating Lipid Levels in Mexican Americans: The Insulin Resistance Atherosclerosis Family Study (IRASFS)
Tools (4):
SOLAR, ADMIXTURE, famSKAT, ANNOVAR
Topics (4):
WGS analysis, Arterial Occlusive Diseases, Sterols, Steroids
Genetic Ancestry of Hadza and Sandawe Peoples Reveals Ancient Population Structure in Africa
Tools (3):
PLINK, VCFtools, ADMIXTURE
Topics (3):
WGS analysis, Homo sapiens, Guizotia abyssinica
Origins and genetic legacies of the Caribbean Taino
Tools (3):
EIGENSOFT, FigTree, ADMIXTURE
Topics (3):
De novo sequencing analysis, WGS analysis, Homo sapiens
Effective population size and the genetic consequences of commercial whaling on the humpback whales (Megaptera novaeangliae) from Southwestern Atlantic Ocean
Tools (3):
Arlequin, NeEstimator, DIYABC
Topics (5):
Population genetic analysis, Megaptera novaeangliae, Biogenic Amines, Amino Alcohols, Catecholamines
Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe
Tools (3):
ADMIXTURE, BEAGLE, TreeMix
Topics (5):
De novo sequencing analysis, Population genetic analysis, WGS analysis, Hemisus marmoratus, Homo sapiens
Adaptation of Arabidopsis thaliana to the Yangtze River basin
Tools (5):
SAMtools, GATK, ADMIXTURE, EIGENSOFT, PHYLIP
Topics (2):
WGS analysis, Arabidopsis thaliana
Domestication Genomics of the Open-Pollinated Scarlet Runner Bean (Phaseolus coccineus L.)
Tools (3):
FastTree, SplitsTree, ADMIXTURE
Topics (4):
WGS analysis, De novo sequencing analysis, Phaseolus vulgaris, Proteus vulgaris
Genetic origins of the Minoans and Mycenaeans
Tools (3):
EIGENSOFT, ADMIXTURE, PLINK
Topics (1):
WGS analysis
Effective Dispersal of Caribbean Reef Fish is Smaller than Current Spacing Among Marine Protected Areas
Tools (3):
ADMIXTURE, Genodive, GenAlEx
Topics (3):
Population genetic analysis, Acids, Acyclic, Sulfhydryl Compounds
Paleogenomic Evidence for Multi-generational Mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the Lower Danube Basin
Tools (9):
GATK, ADMIXTURE, EIGENSOFT, SAMtools, Tablet, HaploGrep, PLINK, mapDamage, HIrisPlex
Topics (2):
WGS analysis, Homo sapiens
Transcriptional mechanisms underlying life‐history responses to climate change in the three‐spined stickleback
Tools (3):
BCL2FASTQ Conversion Software, GemTools, GEM-Mapper
Topics (3):
WGS analysis, De novo sequencing analysis, Gasterosteus aculeatus
A fine structure genetic analysis evaluating ecoregional adaptability of a Bos taurus breed (Hereford)
Tools (3):
ADMIXTURE, Clumpak, GenAlEx
Topics (1):
Population genetic analysis
Postglacial recolonization shaped the genetic diversity of the winter moth (Operophtera brumata) in Europe
Tools (4):
Genodive, Genepop, SplitsTree, DIYABC
Topics (3):
De novo sequencing analysis, WGS analysis, Operophtera brumata
Genetic evidence challenges the native status of a threatened freshwater fish (Carassius carassius) in England
Tools (3):
Genepop, adegenet, DIYABC
Topics (3):
Population genetic analysis, Carassius carassius, Homo sapiens
Identification of a novel locus associated with skin colour in African-admixed populations
Tools (3):
GGV, PLINK, ADMIXTURE
Topics (2):
WGS analysis, Nucleotides
Population genetic structure and adaptation of malaria parasites on the edge of endemic distribution
Tools (3):
Genepop, GenAlEx, ADMIXTURE
Topics (5):
Population genetic analysis, Homo sapiens, Plasmodium falciparum, Infection, Malaria
Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry
Tools (4):
BCL2FASTQ Conversion Software, VCFtools, PLINK, ADMIXTURE
Topics (2):
WGS analysis, Homo sapiens
Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea
Tools (3):
fastPHASE, ADMIXTURE, GAPIT
Topics (3):
WGS analysis, Glycine max, Phytophthora sojae
East Eurasian ancestry in the middle of Europe: genetic footprints of Steppe nomads in the genomes of Belarusian Lipka Tatars
Tools (3):
EIGENSOFT, ADMIXTURE, BEAGLE
Topics (3):
WGS analysis, De novo sequencing analysis, Population genetic analysis
