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Association mapping software tools | Genome-wide association analysis

In the recent years, in order to dissect complex quantitative traits and identify candidate genes affecting such traits, the association mapping approach has been widely used (Hall et al., 2010; Myles et al., 2009; Semagn et al., 2010; Zhu et al.,…
PLINK
Desktop

PLINK

A free, open-source whole genome association analysis toolset, designed to…

A free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on…

BOLT-LMM
Desktop

BOLT-LMM

Requires only a small number of O(MN)-time iterations and increases power by…

Requires only a small number of O(MN)-time iterations and increases power by modeling more realistic, non-infinitesimal genetic architectures via a Bayesian mixture prior on marker effect sizes.…

EMMAX
Desktop

EMMAX

A variance component approach that reduces the computational time for analyzing…

A variance component approach that reduces the computational time for analyzing large GWAS data sets from years to hours. EMMAX outperforms both principal component analysis and genomic control in…

GenABEL
Desktop

GenABEL

An R library for genome-wide association (GWA) analysis. GenABEL implements…

An R library for genome-wide association (GWA) analysis. GenABEL implements effective storage and handling of GWA data, fast procedures for genetic data quality control, testing of association of…

PERGOLA
Desktop

PERGOLA

Provides tools for linkage mapping in polyploids. PERGOLA is a fast…

Provides tools for linkage mapping in polyploids. PERGOLA is a fast deterministic method to calculate the order of markers in a linkage group. It creates correct linkage groups, marker orders and…

SeqFeatR
Desktop
Web

SeqFeatR

An open source software SeqFeatR has been developed to identify associations…

An open source software SeqFeatR has been developed to identify associations between mutation patterns in biological sequences and specific selection pressures ("features"). SeqFeatR allows…

NAM
Desktop

NAM

An R package that allows user to take into account prior information regarding…

An R package that allows user to take into account prior information regarding population stratification to relax the linkage phase assumption of current methods. NAM allows markers to be treated as…

PCAN
Desktop

PCAN Phenotype Consensus ANalysis

A phenotype-based method to support the identification of disease genes by…

A phenotype-based method to support the identification of disease genes by evaluating whether similar phenotypes are linked to genes in the same signaling neighborhood. PCAN allows the user to…

The Implicitome
Desktop

The Implicitome

A resource for rationalizing gene-disease associations. The implicitome can be…

A resource for rationalizing gene-disease associations. The implicitome can be used in conjunction with experimental data resources to rationalize both known and novel associations. We demonstrate…

eRD-GWAS
Desktop

eRD-GWAS

Permits gene expression level to be tested as an explanatory variable during…

Permits gene expression level to be tested as an explanatory variable during genome-wide association studies (GWAS). eRD-GWAS employs a Bayesian-based statistical method. It utilizes RNA-seq…

CropQuant
Desktop

CropQuant

Integrates hardware with open source software capable of complex analytic…

Integrates hardware with open source software capable of complex analytic solutions. CropQuant is an automated field phenotyping platform that provides researchers with a toolkit allowing to fulfil…

treeWAS
Desktop

treeWAS

Controls for the disruptive effects of both population structure and…

Controls for the disruptive effects of both population structure and recombination. treeWAS is a phylogenetic approach that is able to overcome many of the limitations of existing microbial genome…

GWASTools
Desktop

GWASTools

An R/Bioconductor package for quality control and analysis of genome-wide…

An R/Bioconductor package for quality control and analysis of genome-wide association studies (GWAS). GWASTools brings the interactive capability and extensive statistical libraries of R to GWAS.…

QSAT
Desktop

QSAT Quantitative Similarity-based Association Test

Identifies association between a candidate marker and a quantitative trait of…

Identifies association between a candidate marker and a quantitative trait of interest, through use of unrelated individuals. QSAT is a quantitative similarity-based association test that controls…

GWAPP
Desktop
Web

GWAPP

Enables researchers working with Arabidopsis thaliana to do genome wide…

Enables researchers working with Arabidopsis thaliana to do genome wide association mapping (GWAS) on their phenotypes. GWAPP features an extensive, interactive, and user-friendly interface that…

Matapax
Web

Matapax

An online platform designed to make association studies easier to perform for…

An online platform designed to make association studies easier to perform for key organisms. Simply upload the trait measurements and Matapax will do the rest. Currently, Matapax can be used to…

Scoary
Desktop

Scoary

A tool for pan-genome wide association studies (GWAS). Scoary is designed to…

A tool for pan-genome wide association studies (GWAS). Scoary is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the…

GWASpi
Desktop

GWASpi Genome Wide Association Study pipeline

A user-friendly, multiplatform, desktop-able application for the management and…

A user-friendly, multiplatform, desktop-able application for the management and analysis of GWAS data, with a novel approach on database technologies to leverage the most out of commonly available…

GAPIT
Desktop

GAPIT Genome Association and Prediction Integrated Tool

Implements advanced statistical methods including the compressed mixed linear…

Implements advanced statistical methods including the compressed mixed linear model (CMLM) and CMLM-based genomic prediction and selection. The GAPIT package can handle large datasets in excess of 10…

GLOGS
Desktop

GLOGS Genome-wide LOGistic mixed model/Score test

A mixed model-based system for GWAS of binary traits in populations with…

A mixed model-based system for GWAS of binary traits in populations with related individuals. GLOGS performs a GWAS by (1) estimating parameters of a logistic risk model based on non-genetic…

TASSEL
Desktop

TASSEL Trait Analysis by aSSociation, Evolution and Linkage

Implements general linear model and mixed linear model approaches for…

Implements general linear model and mixed linear model approaches for controlling population and family structure. For result interpretation, the program allows for linkage disequilibrium statistics…

EMMA
Desktop

EMMA Efficient Mixed-Model Association

Corrects for population structure and genetic relatedness in model organism…

Corrects for population structure and genetic relatedness in model organism association mapping. EMMA takes advantage of the specific nature of the optimization problem in applying mixed models for…

OGA
Desktop

OGA Ontological tool of phenotypes with Genetic Associations

Allows users to perform meaningful tests that take advantage of the ontology.…

Allows users to perform meaningful tests that take advantage of the ontology. OGA offers a way to find specific phenotypes and browse the ontology. It stores about 2 300 concepts linked to a total of…

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