Genetic linkage analysis software tools | Genome-wide association study
For many years, linkage analysis was the primary tool used for the genetic mapping of Mendelian and complex traits with familial aggregation. Linkage analysis was largely supplanted by the wide adoption of genome-wide association studies (GWASs). However, with the recent increased use of whole-genome sequencing (WGS), linkage analysis is again emerging as an important and powerful analysis method for the identification of genes involved in disease aetiology, often in conjunction with WGS filtering approaches.
Allows analysis of genetic data. PowerMarker allows users to increase speed time for analysis lifecycle and offers a way to maintain data integrity throughout the process. It can be used to manage data, to conduct analysis and provides a good solution to display data.
Provides an interactive, user-friendly environment designed to let a geneticist easily explore data. MAPMAKER uses the Lander-Green algorithm to calculate the “best” map for any given order of loci. It makes it practical to study a large number of loci simultaneously. This tool includes an interactive command language which allows one to compare different genetic orders and to map new loci to genetic intervals.
A method for the analysis of dense genetic maps in pedigree data that provides extremely fast solutions to common problems such as allele-sharing analyses and haplotyping. Merlin is a computer program that uses sparse inheritance trees for pedigree analysis. It performs rapid haplotyping, genotype error detection and affected pair linkage analyses and can handle more markers than other pedigree analysis packages.
A program for detecting marker typing incompatibilities in pedigree data. PedCheck assists researchers in identifying all Mendelian inconsistencies in pedigree data and will provide them with useful and detailed diagnostic information to help resolve the errors.
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.
Assesses the null hypothesis of linkage equilibrium (LE) for multilocus data. LIAN is based on a Monte Carlo method and an algebraic approach to perform the hypothesis test. It first proceeds by calculating the number of loci at which each pair of haplotypes differs. This web-application then generates pairwise distances between its sampled taxa members and returns the genetic diversity.
Enables identification of identical and proximate markers between linkage maps. MapComp permits users to compare genetic maps built from related species with or without the same RADseq protocol. It uses a reference genome of a related species as an intermediate This software is able to supply a detailed characterization of the homologous and homeologous chromosome arms representing all major genera included in the salmonid family.