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.
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.
It can handle large pedigrees and an intermediate number of marker loci for parametric and non-parametric multipoint linkage analysis of qualitative and quantitative traits. SimWalk2 uses Markov chain Monte Carlo (MCMC) and simulated annealing algorithms to perform these multipoint analyses.
Enables users to construct large single nucleotide polymorphisms (SNPs) datasets. Lep-MAP assists researchers in linkage mapping of ultra-dense genome-wide SNP data. It utilizes simultaneously data on multiple outbred families. This application is able to consider necessary parameters significance to select them and is also able to increase linkage map accuracy by taking into account of achiasmatic meiosis.
A pedigree reconstruction algorithm that uses estimates of genome-wide identity by descent to reconstruct pedigrees consistent with observed genetic data. However, when genetic data for individuals within a pedigree are missing, often multiple pedigrees can be reconstructed that fit the data. We report a major expansion of PRIMUS that uses mitochondrial (mtDNA) and non-recombining Y chromosome (NRY) haplotypes to eliminate many pedigree structures that are inconsistent with the genetic data. PRIMUS is a permanent solution to identifying the maximum number of unrelated samples for a genetic analysis.
Performs likelihood-based statistical analysis to solve a variety of genetic problems. Implementations are included for all common, and several statistical genetic tests. Data sets can consist of qualitative or quantitative traits, pedigree or population samples, limited loci or dense SNPs. Where appropriate, the analysis will use either the Elston-Stewart or Lander-Green-Kruglyak algorithms, whichever is more efficient for each individual pedigree.
Performs joint linkage and linkage disequilibrium analysis between a marker and a putative disease locus. A key feature of PSEUDOMARKER is that it can combine case-controls and pedigrees of varying structure into a single unified analysis. Thus it maximizes the full likelihood of the data over marker allele frequencies or conditional allele frequencies on disease and recombination fraction.
Uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees. LAMP provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern.
Assists in performing linkage analysis of pedigree data when the target phenotype is ordinal. LOT implements a latent-variable proportional-odds logistic model that allows analysis of the ordinal traits directly. It provides intuitive results by visualizing the significance level of linkage between the markers and the disease trait. It can be employed to study the genetic basis of such complex traits.
Generates the necessary files and performs linkage analysis using several programs, including GeneHunter. Data can be analyzed in sets of markers, in defined centimorgan intervals and by using different allele frequency algorithms. The outputs consist of genome-wide as well as chromosomal postscript plots of LOD scores, NPL scores, P-values and other parameters.
Provides geneticists a suite of genetic analysis utilities and is able to perform analyses that are infeasible elsewhere. The system provides tools for both exact and approximate analysis with a reliable accuracy measure. The system source code is freely available, and an online version is also available, enabling computations using tens of thousands of CPUs. In the online version, each user has a private password-protected account and unauthorized access is prevented to retain data privacy. Users can download their data and delete it from the system at any time. Users with higher privacy concerns can download the system source code and install it on their own clusters.
An extensive, flexible software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN, QTLD, and MGA), and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of multiple quantitative traits and/or discrete traits which may involve multiple loci (oligogenic analysis), dominance effects, household effects, and interactions.
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.
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 the very rapid extraction of complete multipoint inheritance information from pedigrees of moderate size. This information is then used in exact computation of multipoint LOD scores and in a powerful method of non-parametric linkage analysis. Quick calculations involving dozens of markers, even in pedigrees with inbreeding and marriage loops, is possible with GENEHUNTER. In addition, the multipoint inheritance information allows the reconstruction of maximum-likelihood haplotypes for all individuals in the pedigree and information content mapping which measures the fraction of the total inheritance information extracted from the marker data.
Analyzes heterogeneity with respect to single marker loci or known maps of markers. HOMOG permits to carrie out homogeneity test for alternative hypothesis. It is able to determine the highest Ln likelihood, Lmax, under the most general alternative hypothesis.
Allows the recombination fractions and preferential pairing factors to be estimated simultaneously. Allomap6 has two major functionalities, computer simulation and real-data analysis. A new linkage analysis model for allotetraploids has been developed by incorporating the fact that homologous and homoeologous pairings occur simultaneously, but at different frequencies, described by the preferential pairing factor.
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.
Assists users in analyzing multiple tightly linked markers. Multiple TDT is a statistical method developed to perform a transmission/disequilibrium test (TDT). It can also investigate multisite parental transmission data. This method was applied to study genetic linkage between the dopamine D2 receptor locus (DRD2) and alcoholism. It can also be used as a valid test for the null hypothesis of no linkage.