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Quantitative trait locus mapping software tools

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…
RASQUAL
Desktop

RASQUAL Robust Allele-Specific Quantitation and Quality Control

Maps quantitative trait loci (QTLs) for sequenced based cellular traits by…

Maps quantitative trait loci (QTLs) for sequenced based cellular traits by combining population and allele-specific signals. RASQUAL is a statistical method, which integrates between-individual…

JoinMap
Desktop

JoinMap

Allows to generate charts of linkage maps and quantitative trait loci (QTLs).…

Allows to generate charts of linkage maps and quantitative trait loci (QTLs). JoinMap permits to export these charts to word processing or presentation software. Several maps can be opened…

SysGenSIM
Desktop

SysGenSIM

Simulates Systems Genetics (SG) experiments in model organisms. SysGenSIM aims…

Simulates Systems Genetics (SG) experiments in model organisms. SysGenSIM aims to evaluate and compare statistical and computational methods and their implementations for analyses of SG data. It…

Animal QTLdb
Dataset

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…

Pheno2Geno
Desktop

Pheno2Geno

Creates genetic maps out of phenotype expression data. Pheno2Geno is made for…

Creates genetic maps out of phenotype expression data. Pheno2Geno is made for high-throughput generation of genetic markers and maps from molecular phenotypes. It selects suitable phenotypes that…

solarius
Desktop

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…

dslice
Desktop

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…

FlexQTL
Desktop

FlexQTL

Allows to proceed Quantitative Trait Loci (QTL) analysis. FlexQTL is based on a…

Allows to proceed Quantitative Trait Loci (QTL) analysis. FlexQTL is based on a Bayesian QTL mapping method and allows three different genotypes, and a continuous uniform distribution to assign prior…

EBEN
Desktop

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…

FastQTL
Desktop

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…

RiceGeneThreshe…
Dataset

RiceGeneThresher

A public online resource for mining genes underlying genome regions of interest…

A public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome.

PEPIS
Web

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…

QGene
Desktop

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…

WebQTL
Web

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…

WormQTL(HD)
Dataset

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…

CottonGen
Dataset

CottonGen

A curated and integrated web-based relational database providing access to…

A curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker…

GDR
Dataset

GDR Genome Database for Rosaceae

A central repository of curated and integrated genetics and genomics data of…

A central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry.

lme4qtl
Desktop

lme4qtl

Provides new method for genetic studies. This extension of lme4 unlocks the…

Provides new method for genetic studies. This extension of lme4 unlocks the well-established lme4 framework for specific quantitative trait locus (QTL) mapping analysis. Lme4qtl adopts its features…

veqtl-mapper
Desktop

veqtl-mapper

Identifies single nucleotide polymorphisms (SNPs) associated with variance of…

Identifies single nucleotide polymorphisms (SNPs) associated with variance of gene expression measurements, which can indicate underlying gene-environment, epistasis or parent of origin effects.…

HpQTL
Desktop

HpQTL

Allows specific quantitative trait loci mediating heterophyllous variation to…

Allows specific quantitative trait loci mediating heterophyllous variation to be mapped throughout the genome. HpQTL is an R package for quantitative trait locus (QTL) analysis in case of highly…

BIP
Dataset

BIP Brassica Information Portal

Centralises phenotypic data from Brassica in a repository. BIP is an open…

Centralises phenotypic data from Brassica in a repository. BIP is an open access and open source project, built on the schema of CropStoreDB, and as such can provide trait data management strategies…

QMSim
Desktop

QMSim

Simulates large-scale genotyping data in multiple and complex livestock…

Simulates large-scale genotyping data in multiple and complex livestock pedigrees. QMSim helps to validate new approaches for fine mapping and genomic selection. The simulation is basically carried…

LINKPHASE
Desktop

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.

QTLMiner
Web

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…

ms2gs
Desktop

ms2gs

Reads genome data from ms file format and performs forward simulation to…

Reads genome data from ms file format and performs forward simulation to evaluate genomic selection scenarios. Ms2gs is a combined coalescence - gene dropping (i.e. backward–forward) simulator for…

R/qtlcharts
Desktop

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…

Qtltools
Desktop

Qtltools

Integrates all functionalities required to easily and rapidly transform raw…

Integrates all functionalities required to easily and rapidly transform raw sequence data into collections of molecular quantitative trait locus (molQTLs). Qtltools is based on powerful methods that…

PruneDIRECT
Desktop

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,…

PhenoMiner
Dataset

PhenoMiner

Provides organized and retrievable quantitative phenotype data curated from…

Provides organized and retrievable quantitative phenotype data curated from different rat research laboratories. PhenoMiner comprises results from National BioResource Project in Japan (NBRP), the…

R/qtl
Desktop

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.

PGDBj
Dataset

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…

TGRD
Dataset

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…

Marker2sequence
Desktop

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…

GridQTL
Web

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…

QTLBIM
Desktop

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…

QTLNetwork
Desktop
Web

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…

Pseudomarker
Desktop

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…

RiceQTLPro
Dataset

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…

MapQTL
Desktop

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…

MAPfastR
Desktop

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…

QTLMap
Desktop

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…

Gramene QTL…
Dataset

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…

MultiQTL
Desktop

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…

PLABQTL
Desktop

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…

QTL…
Desktop

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…

QTLNetworkR
Desktop

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…

EXPLoRA-web
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…

PGMapper
Web

PGMapper

Matches automatically phenotype to genes from a defined genome region or a…

Matches automatically phenotype to genes from a defined genome region or a group of given genes. PGMapper combines the mapping information from the Ensembl database and gene function information from…

BQTL
Desktop

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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