Quantitative trait locus mapping software tools | Genome-wide association study data analysis
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 established to dissect the phenotypic variation into several genomic regions, which greatly facilitated the downstream candidate genes discovery and cloning.
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 differences, allele specific (AS) signals and technical biases in sequencing-based cell phenotypes. It can also highlight genomic regions with problematic AS signals, enabling more informed downstream analysis. Additionally, by minimising the amount of data removed, RASQUAL avoids inadvertent removal of real signal.
Allows users to map quantitative trait locus (QTL) in experimental crosses. R/qtl is a comprehensive QTL mapping toolbox for the analysis of experimental populations. The software provides several methods for various experimental cross types. It includes permutation strategies for determining thresholds of significance relevant for QTL and QTL hot spots.
Conducts whole-genome investigation at many levels-from differences in NR2B mRNA levels to differences in open-field activity levels. WebQTL is based on sophisticated gene mapping methods to proceed. It can serve to study variation in gene expression; map upstream gene loci that modulate transcript levels; and explore networks of genetic correlations among about 100 000 transcript assays.
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 sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable.
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) mapping based on a hidden Markov model. The application offers a graphic user interface that includes features permitting to display clustering of single nucleotide polymorphisms as well as phase calling.
Describes how quantitative trait loci (QTLs) determine interspecies competition and cooperation in a community. CoCoM analyzes markers from different species throughout their genomes and returns combinations of QTLs. It can depict complete picture of genetic architecture by highlighting neglected indirect and genome-genome epistatic genetic effects of QTLs. This tool employs a dynamic model that capitalizes on time series phenotypic data to retrieve interactions.
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 phasing programs designed for large half-sibs families, genotyping and map errors; (ii) DAGPHASE for phasing and clustering the haplotypes, and (iii) DUALPHASE that groups the previews functions.
Allows mining of genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. RiceGeneThresher is a resource built from the public domain databases on rice that involve genetic information, genome annotation, expressed sequence tags (ESTs), protein information, prediction of protein-protein interaction and stress-responsive genes. Users can (i) mine genome region of interest by submitting DNA marker names or DNA sequences or (ii) query genes by gene locus names or gene annotation keywords.
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 genome-scale experimental approaches. It accepts a list of GenBank accession numbers and mRNA RefSeq numbers for genes of interest and generates a results file showing genes positions and information about the corresponding QTL.
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 bulk segregant analysis (BSA). EXPLoRA-web enables easy data upload and parallel processing of different parameter configurations.
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 tool includes bottom-up and top-down biological annotation data and genome criteria from several repositories. It assists users for finding true positive causal gene with the proximity to the sentinel variant.
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 computing, data loading and significant QTLs reporting. It chooses automatically the type of longitudinal curve and covariance matrix by information criterion. This pipeline is designed to work on experimental populations derived from a cross between two inbred lines.
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 simultaneously, each in their own subwindow (a subwindow consists of two tab sheets). It displays charts of a series of linkage groups, which consists of a vertical bar on which the map positions and names of loci are indicated. Such map files can be exported by JoinMap.
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 quantitative trait loci (QTL) with individual effects, epistasis and QTL-environment interaction. Currently, it is able to handle data from F(2), backcross, recombinant inbred lines and double-haploid populations, as well as populations from specific mating designs (immortalized F(2) and BC(n)F(n) populations).
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 permutations is modeled using beta distributions trained from a few permutations and from which adjusted p-values can be estimated at any level of significance with little computational cost. FastQTL also provides a modular base onto which new functionalities are being implemented, such as fine mapping of causal variants, conditional analysis to discover multiple independent QTLs per phenotype and interaction analysis to discover sex or disease specific QTLs.
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 out in two steps: (i) a historical population is simulated to establish mutation-drift equilibrium, (ii) recent population structures are generated. The tool integrates efficient and fast algorithms, which lead to high computing performance.
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 can handle continuous, binary and ordinal traits.
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 implemented in SOLAR. It automates such routine operations as formatting pedigree and phenotype data. It also parses the model output and contains summary and plotting functions for exploration of the results. In addition, solarius enables parallel computing of the linkage and association analyses, that makes the calculation of genome-wide scans more efficient.
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 facilitate the use of dynamic slicing method in bioinformatic applications such as quantitative trait loci (QTLs) study and gene set enrichment analysis.