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Population structure detection software tools | Population genomics

Tools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. However, inferring population structure in large modern data sets imposes severe computational challenges.Source…
STRUCTURE
Desktop

STRUCTURE

A free software package for using multi-locus genotype data to investigate…

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,…

TreeMix
Desktop

TreeMix

Infers patterns of population splits and mixtures from genome-wide allele…

Infers patterns of population splits and mixtures from genome-wide allele frequency data. TreeMix is a unified model that uses the composite likelihood in to search for the maximum likelihood graph.…

NewHybrids
Desktop

NewHybrids

Provides a way to use genetic data to identify species hybrids. NewHybrids is…

Provides a way to use genetic data to identify species hybrids. NewHybrids is applicable not only to loci with fixed differences between species, but also to loci without fixed differences. Though…

hybriddetective
Desktop

hybriddetective

Develops for detection, with estimates of efficiency and accuracy, of…

Develops for detection, with estimates of efficiency and accuracy, of multi-generational hybrid individuals using genetic or genomic data in conjunction with the program NEWHYBRIDS. hybriddetective…

pophelper
Web
Desktop

pophelper

Allows to analyse and visualise population structure. pophelper supports output…

Allows to analyse and visualise population structure. pophelper supports output run files generated from population analysis programs such as STRUCTURE, TESS and numeric delimited formats such as…

EIGENSOFT
Desktop

EIGENSOFT

Uses principal components analysis to explicitly model ancestry differences…

Uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate…

LFA
Desktop

LFA Logistic Factor Analysis

A method for a principal component analysis (PCA) analogue on binomial data via…

A method for a principal component analysis (PCA) analogue on binomial data via estimation of latent structure in the natural parameter. LFA seeks to directly model the logit transformation of…

genepopedit
Desktop

genepopedit

Assists users in manipulation of large multilocus molecular datasets.…

Assists users in manipulation of large multilocus molecular datasets. Functionality can be divided among diagnostic-, manipulation-, sampling-, simulation-, and transformation-based tools. Metadata…

NetStruct
Desktop

NetStruct

Analyzes genetic data in order to infer population structure. It is based on…

Analyzes genetic data in order to infer population structure. It is based on network theory concepts such as community and modularity. NetStruct works with individual genetic data (single nucleotide…

IPCAPS
Desktop

IPCAPS Iterative Pruning to CApture Population Structure

Analyzes single nucleotide polymorphisms (SNP) data to detect fine scale…

Analyzes single nucleotide polymorphisms (SNP) data to detect fine scale structure in samples. IPCAPS is based on the iterative pruning Principal Component Analysis (ipPCA). The package clusters…

BioMiCo
Desktop

BioMiCo Bayesian inference of Microbial Communities

Represents a predictive model for microbiome composition data. BioMiCo…

Represents a predictive model for microbiome composition data. BioMiCo facilitates interpretation of a community structure in light of user-defined feature labels. It is a hierarchical model that can…

StrAuto
Desktop

StrAuto

Integrates STRUCTURE analysis with post-processing using a pipeline approach in…

Integrates STRUCTURE analysis with post-processing using a pipeline approach in addition to implementing parallel computation. StrAuto is a Python program to streamline population structure analysis…

parallelnewhybr…
Desktop

parallelnewhybrid

Provides a substantial decrease in the time required to validate and conduct…

Provides a substantial decrease in the time required to validate and conduct hybrid detection by enabling the parallelization of analyses using NEWHYBRIDS. parallelnewhybrid enables the exploration…

GppFst
Desktop

GppFst

Generates theoretical distributions of FST and dXY under the neutral coalescent…

Generates theoretical distributions of FST and dXY under the neutral coalescent model for two populations that accounts for demographic parameters in a probabilistic framework. GppFst is a popular…

HaploPOP
Desktop

HaploPOP

Uses gain of informativeness for assignment (GIA) to build informative…

Uses gain of informativeness for assignment (GIA) to build informative haplotypes for population assignment. HaploPOP needs reference individuals whose population of origin is known. Based on these…

PSIKO
Desktop

PSIKO Population Structure Inference using Kernel-pca and Optimisation

A software tool written in C++ for quick and accurate estimation of individual…

A software tool written in C++ for quick and accurate estimation of individual ancestry coefficients of a dataset exhibiting population structure. PSIKO takes as input file in the .geno format, with…

CONE
Desktop

CONE Community Oriented Network Estimation

Offers a graph-construction method. CONE can identify an appropriate model for…

Offers a graph-construction method. CONE can identify an appropriate model for a neighborhood selection scheme. It is able to select an appropriate tuning parameter for LASSO with stability-based…

StructureSelect…
Web

StructureSelector

Calculates “K” estimators. StructureSelector is a web based software which…

Calculates “K” estimators. StructureSelector is a web based software which aims to help in selecting and visualizing of the best estimators across a targeted file. The software includes MedMedK,…

PaM
Web
Desktop

PaM Pair Matcher

Allows pairing optimisation using demographic and genetic data. PaM is a…

Allows pairing optimisation using demographic and genetic data. PaM is a genetic-based tool that optimises pairing assignments a priori- and\or posteriori to the trial. The software models individual…

EBG
Desktop

EBG

Includes implementations of the autopolyploid (diseq), allopolyploid (alloSNP),…

Includes implementations of the autopolyploid (diseq), allopolyploid (alloSNP), Hardy Weinberg (hwe), and GATK-like (gatk) models for genotyping in polyploids. ebg is a software for estimating…

PGS
Desktop

PGS Population-based Genome Structure

Generates a population of 3D genome structures where each domain is represented…

Generates a population of 3D genome structures where each domain is represented as a sphere. PGS is a user-friendly software package that runs on local machines and high performance computing…

OriGen
Desktop

OriGen

Adapts techniques from image reconstruction that encourages smoothness without…

Adapts techniques from image reconstruction that encourages smoothness without requiring rigidly parameterized allele frequency surfaces. OriGen is model based and fast. It can infer the geographic…

PSMix
Desktop

PSMix Population Structure inference via MIXture model

Uses for population stratification and individual admixture. PSMIX is an R…

Uses for population stratification and individual admixture. PSMIX is an R package based on maximum likelihood method using expectation-maximization algorithm. PSMIX can be used in population…

GeneClass
Desktop

GeneClass

Computes various genetic assignment criteria to assign or exclude reference…

Computes various genetic assignment criteria to assign or exclude reference populations as the origin of diploid or haploid individuals, as well as of groups of individuals, on the basis of…

NetView
Desktop

NetView

Identifies and allows to visualize fine-scale population structures from a…

Identifies and allows to visualize fine-scale population structures from a genetic relationship matrix among individuals/populations. NetView is an analysis pipeline which combines three different…

NTSYSpc
Desktop

NTSYSpc Numerical Taxonomy and Multivariate analysis System

Allows users to find pattern and structure in multivariate data. NTSYSpc…

Allows users to find pattern and structure in multivariate data. NTSYSpc assists users to calculate a phylogenetic tree that uses the neighbor-joining or unweighted pair-group method with averaging…

TreeClimber
Desktop

TreeClimber

Compares microbial community structures in a rapid, easy-to-use, and…

Compares microbial community structures in a rapid, easy-to-use, and streamlined manner. TreeClimber is adaptation to a method used in population genetics, the parsimony test, to determine the…

AdmixKJump
Desktop

AdmixKJump

A powerful approach to classify population structure. AdmixKJump has more power…

A powerful approach to classify population structure. AdmixKJump has more power to detect the number of populations in a cohort of samples with smaller sample sizes and shorter divergence times.

StructHDP
Desktop

StructHDP

A program for automatically inferring the population structure and number of…

A program for automatically inferring the population structure and number of clusters from a sample of admixed genotype data. StructHDP extends the model used by Structure to allow for a potentially…

mStruct
Desktop

mStruct

A software tool for the detection of population structure in the presence of…

A software tool for the detection of population structure in the presence of admixing and mutations from multi-locus genotype data. mStruct is a mixed membership model (also referred to as an…

strplot
Web
Desktop

strplot Structure Plot

Allows to draw STRUCTURE bar plots. Structure Plot generates publication ready,…

Allows to draw STRUCTURE bar plots. Structure Plot generates publication ready, aesthetic STRUCTURE bar plots by using individual Q matrix from STRUCTURE or CLUMPP output. The program is simple to…

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…

Structure…
Web
Desktop

Structure Harvester

Collates results generated by the program STRUCTURE. Structure Harvester…

Collates results generated by the program STRUCTURE. Structure Harvester provides a fast way to assess and visualize likelihood values across multiple values of K and hundreds of iterations for…

Genodive
Desktop

Genodive

Analyses clonal diversity in asexually reproducing organisms. First,…

Analyses clonal diversity in asexually reproducing organisms. First, differences in clonal diversity between pairs of populations can be tested through bootstrapping; resampling, with replacement,…

HANA
Web

HANA Haplotype ANAlyzer

A haplotype analyzer for the Czech population. HANA needs haplotype in National…

A haplotype analyzer for the Czech population. HANA needs haplotype in National Marrow Donor Program format (NMDP) and generates graphic of haplotype probabilities.

IP2CAPS
Desktop

IP2CAPS

A framework for population or patient structure analysis where genetic…

A framework for population or patient structure analysis where genetic determinants of admixture are organized according to highly complex architectures. IP2CAPS allows biologists to analyze…

SiuEtAl2012
Algorithm

SiuEtAl2012

Provides a statistic method for human population structure studies. The…

Provides a statistic method for human population structure studies. The software intends to study association in the population structure by combining genomic information in a genomic region. It was…

Genotype
Desktop

Genotype

Assigns individuals to clonal lineages. Genotype can handle data from different…

Assigns individuals to clonal lineages. Genotype can handle data from different kinds of genetic markers, both codominant and dominant, such as allozymes, microsatellites, amplified fragment length…

hybridlab
Desktop

hybridlab

Simulates intraspecific hybrids from population samples of nuclear genetic…

Simulates intraspecific hybrids from population samples of nuclear genetic markers such as microsatellites, allozymes or SNPs (single nucleotide polymorphisms). From standard population genetic data…

AFLPOP
Desktop

AFLPOP

Allocates and simulates population by using amplified fragment length…

Allocates and simulates population by using amplified fragment length polymorphism markers. AFLPOP is an adaptation of Paetkau’s method for co-dominant alleles. It can provide information on the…

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