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.
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 interval mapping), or with a nonparametric method.
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.
Aligns quantitative traits using a map of molecular markers. QTL Cartographer employs linear regression, interval mapping, composite interval mapping, and multiple interval mapping methods to work. It can fit and compare a host of statistical models to quantitative trait locus (QTL)-environment interactions, and close linkage. This tool enables users to simulate, reformat or investigate data and display the results of the analyses.
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.
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.
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).
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 higher resolution detection of QTL; an Epistasis option for 2-QTL determination in F2 populations was also implemented. This functionality was offered via a web portal which offered data persistence for management of users' output and distributed execution of analyses via a computational Grid system.