Mapping quantitative trait loci (QTL) for complex traits has become a routine tool in functional genomic research. With the advent of highly dense genetic maps of various organisms, a large number of systemic statistical approaches and the corresponding software have been…
Desktop app
QGene QGene

QGene

Allows execution and comparison of a variety of modern QTL-mapping methods and…

Allows execution and comparison of a variety of modern QTL-mapping methods and supports third-party addition of new ones. QGene accommodates line-cross mating designs consisting of any arbitrary…

Desktop app
Empirical Bayesian… Empirical Bayesian Elastic Net

EBEN Empirical Bayesian Elastic Net

An empirical Bayesian EN algorithm for multiple QTL mapping that inherits the…

An empirical Bayesian EN algorithm for multiple QTL mapping that inherits the efficiency of the previously developed EBlasso algorithm. Simulation results demonstrated that EBEN provided higher power…

Desktop app
MapQTL MapQTL

MapQTL

Software tool for the mapping of quantitative trait loci in experimental…

Software tool for the mapping of quantitative trait loci in experimental populations of diploid species. Analyse your QTL experiments with interval mapping, with the powerful MQM mapping (=composite…

Web app
Pipeline for… Pipeline for estimating EPIStatic effect

PEPIS Pipeline for estimating EPIStatic effect

A web server-based tool for analysing polygenic epistatic effects. PEPIS is…

A web server-based tool for analysing polygenic epistatic effects. PEPIS is based on a linear mixed model that has been used to predict the performance of hybrid rice. It includes two main…

Desktop app
PruneDIRECT PruneDIRECT

PruneDIRECT

An algorithm for multiple quantitative trait locus (QTL) scan with epistatic…

An algorithm for multiple quantitative trait locus (QTL) scan with epistatic interactions. PruneDIRECT algorithm has specific strengths for permutation testing. It has been integrated to a flexible,…

Desktop app
Marker2sequence Marker2sequence

Marker2sequence

Aims at mining quantitative trait loci (QTLs) for candidate genes.…

Aims at mining quantitative trait loci (QTLs) for candidate genes. Marker2sequence, for each gene, within the QTL region, uses data integration technology to integrate putative gene function with…

Plant Genome DataBase… Plant Genome DataBase Japan

PGDBj Plant Genome DataBase Japan

Aims to integrate plant genome-related information from databases (DBs) and the…

Aims to integrate plant genome-related information from databases (DBs) and the literature. The PGDBj is comprised of three component DBs and a cross-search engine, which provides a seamless search…

Desktop app
solarius solarius

solarius

Performs linkage and association mappings of the quantitative trait loci (QTLs)…

Performs linkage and association mappings of the quantitative trait loci (QTLs) in pedigrees of arbitrary size and complexity. solarius allows the user to exploit the variance component methods…

Desktop app
FastQTL FastQTL

FastQTL

Implements a popular cis-QTL mapping strategy in a user- and cluster-friendly…

Implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool. FastQTL also proposes an efficient permutation procedure to control for multiple testing. The outcome of…

Desktop app
dslice dslice

dslice

Many statistical problems in bioinformatics and genetics can be formulated as…

Many statistical problems in bioinformatics and genetics can be formulated as the testing of associations between a categorical variable and a continuous variable. dslice is an R package to…

Desktop app
MAPfastR MAPfastR

MAPfastR

A software package developed to analyze quantitative trait loci data from…

A software package developed to analyze quantitative trait loci data from inbred and outbred line-crosses. MAPfastR includes a number of modules for fast and accurate quantitative trait loci…

Desktop app
QTLMap QTLMap

QTLMap

A software tool dedicated to the detection of QTL from experimental designs in…

A software tool dedicated to the detection of QTL from experimental designs in outbred population. The statistical techniques used are linkage analysis (LA) and linkage disequilibrium linkage…

RiceQTLPro RiceQTLPro

RiceQTLPro

This database is an integrated web-based system providing information about…

This database is an integrated web-based system providing information about quantitative trait loci (QTL) markers in rice plant. The RiceQTLPro has the three main features namely, (1) QTL markers…

Gramene QTL database Gramene QTL database

Gramene QTL database

Includes QTL identified for numerous agronomic traits in rice, maize, barley,…

Includes QTL identified for numerous agronomic traits in rice, maize, barley, oat, sorghum, pearl millet, foxtail millet and wild rice. The emphasis is on presenting QTLs with both information on…

Web app
GridQTL GridQTL

GridQTL

It was released in the summer of 2006 and extended the functionality of…

It was released in the summer of 2006 and extended the functionality of QTLExpress by adding a Linkage-Disequilibruim-Linkage-Analysis (LDLA) tool in tandem with a Haplotyping analysis to enable…

Desktop app
MultiQTL MultiQTL

MultiQTL

Integrates a broad spectrum of data mining, statistical analysis, interactive…

Integrates a broad spectrum of data mining, statistical analysis, interactive visualization and modeling tools that allow QTL analysis based on advanced and sophisticated methods for maximum…

Desktop app
PLant Breeding And… PLant Breeding And Biology QTL

PLABQTL PLant Breeding And Biology QTL

A software package written for routine QTL analysis. Its main purpose is to…

A software package written for routine QTL analysis. Its main purpose is to localize and characterize QTL in mapping populations derived from a biparental cross by selfing or production of doubled…

Desktop app
Pseudomarker Pseudomarker

Pseudomarker

A set of programs written in MATLAB for the analysis of QTL data from inbred…

A set of programs written in MATLAB for the analysis of QTL data from inbred line crosses. Although Pseudomarker was originally developed based on the multiple imputation genome scan algorithm, it…

Desktop app
QTL Cartographer QTL Cartographer

QTL Cartographer

A suite of programs to map quantitative traits using a map of molecular…

A suite of programs to map quantitative traits using a map of molecular markers. Windows QTL Cartographer is a user friendly version of QTL Cartographer. It has a GUI interface and runs under…

Desktop app
R/qtlcharts R/qtlcharts

R/qtlcharts

An R package to create interactive graphics for experiments to map quantitative…

An R package to create interactive graphics for experiments to map quantitative trait loci (QTL; genetic loci that influence quantitative traits). R/qtlcharts serves as a companion to the R/qtl…

Desktop app
Web app
QTLNetwork QTLNetwork

QTLNetwork

A software package for mapping and visualizing the genetic architecture…

A software package for mapping and visualizing the genetic architecture underlying complex traits for experimental populations derived from a cross between two inbred lines. It can simultaneously map…

Desktop app
QTLNetworkR QTLNetworkR

QTLNetworkR

An R package that aims to provide a user-friendly and platform-independent tool…

An R package that aims to provide a user-friendly and platform-independent tool to visualize quantitative trait loci (QTL) mapping results. The graphical functions of the QTLNetworkR are based upon…

Desktop app
R/qtl R/qtl

R/qtl

A free and powerful software for mapping and exploring quantitative trait loci…

A free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types.

Web app
WebQTL WebQTL

WebQTL

A website that combines databases of complex traits with fast software for…

A website that combines databases of complex traits with fast software for mapping quantitative trait loci (QTLs) and for searching for correlations among traits. WebQTL also includes well-curated…

PhenoMiner PhenoMiner

PhenoMiner

Incorporates quantitative phenotype data for rat strains, in addition to the…

Incorporates quantitative phenotype data for rat strains, in addition to the currently existing qualitative phenotype data for rat strains, QTLs and genes. A specialized curation tool was designed to…

Web app
QTLMiner QTLMiner

QTLMiner

A web server for mining QTL information from tables and plain text found in…

A web server for mining QTL information from tables and plain text found in literature. Heterogeneous and complex tables were converted into a structured database, combined with information extracted…

WormQTL(HD) WormQTL(HD)

WormQTL(HD)

A database that quantitatively and systematically links expression Quantitative…

A database that quantitatively and systematically links expression Quantitative Trait Loci (eQTL) findings in C. elegans to gene-disease associations in man. WormQTL(HD) is a user-friendly set of…

Animal Quantitative… Animal Quantitative Trait Loci database

Animal QTLdb Animal Quantitative Trait Loci database

Strives to collect all publicly available trait mapping data, i.e. QTL…

Strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped to livestock…

Web app
EXPLoRA-web EXPLoRA-web

EXPLoRA-web

A web service wrapped around our previously published algorithm EXPLoRA, which…

A web service wrapped around our previously published algorithm EXPLoRA, which exploits linkage disequilibrium (LD) to increase the power and accuracy of quantitative trait loci identification in…

Tomato Genomic… Tomato Genomic Resources Database

TGRD Tomato Genomic Resources Database

Allows interactive browsing of tomato genes, micro RNAs, simple sequence…

Allows interactive browsing of tomato genes, micro RNAs, simple sequence repeats (SSRs), important quantitative trait loci and Tomato-EXPEN 2000 genetic map altogether or separately along twelve…

Desktop app
QTL Bayesian Interval… QTL Bayesian Interval Mapping

QTLBIM QTL Bayesian Interval Mapping

Provides a Bayesian model selection approach to map multiple interacting QTL.…

Provides a Bayesian model selection approach to map multiple interacting QTL. It works on experimentally inbred lines and performs a genome-wide search to locate multiple potential QTL. The package…

Desktop app
LINKPHASE Deprecated LINKPHASE

LINKPHASE

A phasing program designed for large half-sibs families (as observed in plant…

A phasing program designed for large half-sibs families (as observed in plant and animals) that is robust to genotyping and map errors. The software LINKPHASE3 is included in the PHASEBOOK package.

Desktop app
Bayesian Quantitative… Deprecated Bayesian Quantitative Trait Mapping

BQTL Bayesian Quantitative Trait Mapping

Software tool for the mapping of genetic traits from line crosses and…

Software tool for the mapping of genetic traits from line crosses and recombinant inbred lines. BQTL performs 1) maximum likelihood estimation of multi-gene models, 2) Bayesian estimation of…

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