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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…

Funmap
Desktop

Funmap Functional Mapping

Provides assistance for analyzing quantitative trait loci (QTL) for a…

Provides assistance for analyzing quantitative trait loci (QTL) for a longitudinal trait based on functional mapping. Funmap performs a pipeline service that covers QTLs scanning, significance value…

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…

PHASEBOOK
Desktop

PHASEBOOK

Provides phasing marker genotypes. PHASEBOOK is a package that uses familial…

Provides phasing marker genotypes. PHASEBOOK is a package that uses familial and/or population information. The application contains various features including: (i) LINKPHASE and LINKPHASE3 that are…

TetraploidSNPMa…
Desktop

TetraploidSNPMap

Furnishes a method for computing linkage maps in autotetraploid.…

Furnishes a method for computing linkage maps in autotetraploid. TetraploidsSNPMap is composed of two mains components that allows users to perform linkage analysis and quantitative trait loci (QTL)…

AAOT
Desktop

AAOT Association Analysis of an Ordinal Trait

Turns an ordinal trait to a quantitative trait. AAOT is a SAS program that…

Turns an ordinal trait to a quantitative trait. AAOT is a SAS program that allows users to create a dataset for being analyzed by the FBAT software.

QTL MatchMaker
Web

QTL MatchMaker

Procures a platform for comparative genomics studies of quantitative trait loci…

Procures a platform for comparative genomics studies of quantitative trait loci (QTL) across human, mouse and rat species. QTL MatchMaker enables to analyze large sets of data produced using…

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

Provides quantitative trait loci (QTL) data for cattle, chicken and pigs.…

Provides quantitative trait loci (QTL) data for cattle, chicken and pigs. AnimalQTLdb enables comparison of QTL results within species and across experiments. It serves as a bridge between genotypes…

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…

HyB_BR
Desktop

HyB_BR Hybrid BayesR

Allows users to perform simultaneous genomic prediction and quantitative trait…

Allows users to perform simultaneous genomic prediction and quantitative trait loci (QTL) mapping. Hyb_BR is developed as a hybrid algorithm which combine an Expectation-Maximisation (EM) module and…

Mapfuser
Desktop

Mapfuser

Allows consensus map construction, interpolation of genetic positions,…

Allows consensus map construction, interpolation of genetic positions, estimation of recombination rates, and post-analysis assessment. Mapfuser offers three main applications: (1) quality control,…

LinkageMapView
Desktop

LinkageMapView

Produces publication quality genetic maps. LinkageMapView provides options that…

Produces publication quality genetic maps. LinkageMapView provides options that allow the user to reduce extraneous detail, minimize map dimensions, and highlight areas of importance. It can color…

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…

WormQTL(HD)
Dataset

WormQTL(HD)

Gathers information helping user to predict gene-to-gene association. WormQTL…

Gathers information helping user to predict gene-to-gene association. WormQTL HD is a database assisting in exploitation of the worm expression Quantitative Trait Loci (eQTL) data for human disease…

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…

R/qtl
Desktop

R/qtl

Allows users to map quantitative trait loci (QTL) in experimental crosses.…

Allows users to map quantitative trait loci (QTL) in experimental crosses. R/qtl is a comprehensive QTL mapping toolbox for the analysis of experimental populations. The software provides several…

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…

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.

ProGeM
Desktop

ProGeM Prioritisation of candidate causal Genes at Molecular QTLs

Identifies and prioritizes candidate causal genes at molecular quantitative…

Identifies and prioritizes candidate causal genes at molecular quantitative trait locus (QTL). ProGeM is a configurable analysis script designed for specific trait classes. This gene prioritization…

MVQTLCIM
Desktop

MVQTLCIM

Allows composite interval mapping (CIM) mapping of multiple or longitudinal…

Allows composite interval mapping (CIM) mapping of multiple or longitudinal traits in a full-sib family derived by crossing two outbred parents. MVQTLCIM is a command-based software that implements…

QTLseqr
Desktop

QTLseqr

Provides an R package for Next Generation Sequencing (NGS) and Bulk Segregant…

Provides an R package for Next Generation Sequencing (NGS) and Bulk Segregant Analysis (BSA). QTLseqr can import and filter single nucleotide polymorphism (SNP) data from Genome Analysis Tool Kit…

univariate_dose…
Desktop

univariate_dose_response

Models responses to show interactions between stressors and range of nonlinear…

Models responses to show interactions between stressors and range of nonlinear responses of the system. univariate_dose_response is a tool for surface modelling and shape evaluation method.

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…

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…

PQHE
Desktop

PQHE Pooled QTL Heritability Estimator

Permits pooled quantitative trait loci (QTL) heritability (QH) estimation under…

Permits pooled quantitative trait loci (QTL) heritability (QH) estimation under different experimental designs. PQHE can reflect the structure of the population. It was tested by analyzing four…

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…

solQTL
Dataset

solQTL

Allows quantitative trait loci (QTL) data organization, storage, and analysis.…

Allows quantitative trait loci (QTL) data organization, storage, and analysis. solQTL allows users to upload their QTL population details such as name, description, and parents, trait data,…

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…

QlicRice
Dataset

QlicRice QTL and Loci Interaction Channels in Rice

Captures and integrates genomic information on quantitative trait loci (QTLs)…

Captures and integrates genomic information on quantitative trait loci (QTLs) related to abiotic stresses in rice. QlicRice provides a query interface designed for searching genes underlying QTLs…

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…

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