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Genetic linkage analysis software tools

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).…
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…

Vitesse
Desktop

Vitesse

Computes likelihoods with the functionality of the LINKMAP and MLINK programs…

Computes likelihoods with the functionality of the LINKMAP and MLINK programs from LINKAGE. Vitesse enables fast and precise multipoint mapping of disease loci with highly polymorphic markers.

Merlin
Desktop

Merlin

A method for the analysis of dense genetic maps in pedigree data that provides…

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…

MAPMAKER
Desktop

MAPMAKER

Provides an interactive, user-friendly environment designed to let a geneticist…

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.…

HOMOG
Desktop

HOMOG

Analyzes heterogeneity with respect to single marker loci or known maps of…

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…

LPmerge
Desktop

LPmerge

Resolves ordinal conflicts between linkage maps and eliminates shrinkage of the…

Resolves ordinal conflicts between linkage maps and eliminates shrinkage of the consensus map. LPmerge allows construction of consensus maps across multiple populations through linear programming…

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)…

AlloMap6
Desktop

AlloMap6

Allows the recombination fractions and preferential pairing factors to be…

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…

ALOHOMORA
Desktop

ALOHOMORA

Converts Affymetrix genotype data into linkage and haplotype information.…

Converts Affymetrix genotype data into linkage and haplotype information. ALOHOMORA can perform a comprehensive quality control of the data. It facilitates linkage analysis with chip data. This tool…

LAMP
Desktop

LAMP Linkage and Association Modeling in Pedigrees

Uses a maximum likelihood model to extract information on genetic linkage and…

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…

polymapR
Desktop

polymapR

Allows users to analyze genetic linkage. polymapR is an R package designed for…

Allows users to analyze genetic linkage. polymapR is an R package designed for creating linkage maps for polysomic triploids, tetraploids and hexaploids, accommodating either fully tetrasomic or…

BLINK
Desktop

BLINK Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway

Allows users to control false positives resulted from population structure,…

Allows users to control false positives resulted from population structure, unequal relatedness among individuals and improve statistical power in genome-wide association studies (GWAS). BLINK is a…

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…

FastCMH
Desktop

FastCMH

Discovers genomic regions of contiguous Single Nucleotide Polymorphisms (SNPs)…

Discovers genomic regions of contiguous Single Nucleotide Polymorphisms (SNPs) that are associated to a phenotype of interest under a model of genetic heterogeneity. FastCMH can drastically reduce…

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…

SimWalk2
Desktop

SimWalk2

It can handle large pedigrees and an intermediate number of marker loci for…

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…

designGG
Web
Desktop

designGG

Produces an accurate estimation of the most relevant biological parameters of…

Produces an accurate estimation of the most relevant biological parameters of an experiment. designGG employs the number of experimental factors to be varied, the genotype information on the…

GTEvaluator
Desktop

GTEvaluator Genome Target Evaluator

Ranks the most suitable markers among a list, by calculating their sensitivity…

Ranks the most suitable markers among a list, by calculating their sensitivity and specificity toward a genome dataset. GTEvaluator permits to take rational decision on the choice of genetic markers…

BatchMap
Desktop

BatchMap

Estimates phases and true recombination frequencies in constructing the linkage…

Estimates phases and true recombination frequencies in constructing the linkage map. BatchMap calculates the likelihood for each possible phase of the first marker pair in a sequence of markers. It…

GIGI-Pick
Desktop

GIGI-Pick

Facilitates the evaluation and comparison of subject selection choices in…

Facilitates the evaluation and comparison of subject selection choices in sequencing studies in pedigrees. GIGI-Pick uses a "coverage" as one metric to naturally relate pedigree-based…

Mendel
Desktop

Mendel

Performs likelihood-based statistical analysis to solve a variety of genetic…

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…

GHOST
Web

GHOST Global Hepatitis Outbreak and Surveillance Technology

Provides a platform for monitoring hepatitis C. GHOST allows users to check the…

Provides a platform for monitoring hepatitis C. GHOST allows users to check the quality of next generation sequencing (NGS) data as well as extract information on transmission clusters. It permits to…

MapDisto
Desktop

MapDisto

Concerns the genetic studies. MapDisto is a program for mapping genetic markers…

Concerns the genetic studies. MapDisto is a program for mapping genetic markers in experimental segregating populations like backcross, F2, doubled haploids, RIL (single-seed descent), and highly…

RarePedSim
Desktop

RarePedSim Rare-variant Pedigree-based Simulator

Simulates region/gene-level genotype and phenotype data for complex and…

Simulates region/gene-level genotype and phenotype data for complex and Mendelian traits for any given pedigree structure. Using a genetic model, sequence variant data can be generated either…

PSEUDOMARKER
Desktop

PSEUDOMARKER

Performs joint linkage and linkage disequilibrium analysis between a marker and…

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…

GASP
Desktop

GASP Genometric Analysis Simulation Program

Simulates a trait locus and seven marker loci: one single locus four-allele…

Simulates a trait locus and seven marker loci: one single locus four-allele marker (M0) and six biallelic markers (M1, M2, M3, M4, M5, and M6), with map distance and allele frequencies. The GASP…

SOLAR
Desktop

SOLAR Sequential Oligogenic Linkage Analysis Routines

An extensive, flexible software package for genetic variance components…

An extensive, flexible software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN, QTLD, and MGA), and…

TLINKAGE
Desktop

TLINKAGE

An extension of the general LINKAGE programs for genetic linkage analysis. The…

An extension of the general LINKAGE programs for genetic linkage analysis. The extension consists of allowing for a disease phenotype to be under the control of two loci. The two postulated disease…

PedCheck
Desktop

PedCheck

A program for detecting marker typing incompatibilities in pedigree data.…

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…

GeneHunter
Desktop

GeneHunter

Allows the very rapid extraction of complete multipoint inheritance information…

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…

SEQLinkage
Desktop

SEQLinkage

Implements a collapsed haplotype pattern (CHP) method to generate markers from…

Implements a collapsed haplotype pattern (CHP) method to generate markers from sequence data for linkage analysis. The core concept is that instead of treating each variant a separate marker, we…

PhenoLink
Web

PhenoLink

Links phenotype to omics data sets using well-established as well new…

Links phenotype to omics data sets using well-established as well new techniques. PhenoLink imputes missing values and preprocesses input data (i) to decrease inherent noise in the data and (ii) to…

TSPmap
Desktop

TSPmap

Provides an implementation of the travelling salesperson problem (TSP) for…

Provides an implementation of the travelling salesperson problem (TSP) for generation of genetic maps. TSPmap is an R package that applies TSP algorithms. This application produces low-error maps…

SiNoPsis
Web

SiNoPsis

Characterizes single nucleotide polymorphisms (SNPs) in the context of known…

Characterizes single nucleotide polymorphisms (SNPs) in the context of known annotated human genes or a region defined by genomic coordinates. SiNoPsis presents candidate SNPs related to the…

Lep-MAP
Desktop

Lep-MAP

Constructs accurate linkage maps with ultra-dense genome-wide single nucleotide…

Constructs accurate linkage maps with ultra-dense genome-wide single nucleotide polymorphism (SNP) data. Lep-MAP utilizes simultaneously data on multiple outbred families and can increase linkage map…

Superlink-Onlin…
Desktop
Web

Superlink-Online SNP

Provides geneticists a suite of genetic analysis utilities and is able to…

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…

easyLINKAGE
Desktop

easyLINKAGE

Generates the necessary files and performs linkage analysis using several…

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…

FsLinkageMap
Desktop

FsLinkageMap

Constructs genetic linkage maps with molecular markers generated in a full-sib…

Constructs genetic linkage maps with molecular markers generated in a full-sib family. FsLinkageMap uses a multi-locus linkage analysis which will be beneficial to construct high-density genetic…

SimPed
Desktop

SimPed Pedigree-based Simulator

Generates haplotype and/or genotype data for large number of marker loci…

Generates haplotype and/or genotype data for large number of marker loci regardless of pedigree structure. The SimPed program generates both genotype and haplotype data unconditional on the disease…

MSTMap
Desktop
Web

MSTMap

A software tool that is capable of constructing genetic linkage maps…

A software tool that is capable of constructing genetic linkage maps efficiently and accurately. It can handle various mapping populations including BC1, DH, Hap, and RIL, among others. The tool…

GEDI
Desktop

GEDI Genotype Error Detection and Imputation

Provides methods for error detection in whole-genome single nucleotide…

Provides methods for error detection in whole-genome single nucleotide polymorphism (SNP) genotype data, recovery of missing SNP genotypes and imputation of genotypes at untyped SNPs based on…

GMRP
Desktop

GMRP GWAS-based Mendelian Randomization and Path analyses

Performs correlation and path analyses to construct path diagrams of causal…

Performs correlation and path analyses to construct path diagrams of causal variables to the disease. GMRP can perform analyses of Mendelian Randomization (MR), correlation, path of causal variables…

SLINK
Desktop

SLINK

Allows to carry out such power calculations by simulating genotypes at one…

Allows to carry out such power calculations by simulating genotypes at one locus given the phenotypes at another locus linked with the first locus. SLINK may be used in simulating under no linkage…

GIGI-Check
Desktop

GIGI-Check

Detects Mendelian consistent genotyping errors of dense markers in pedigree…

Detects Mendelian consistent genotyping errors of dense markers in pedigree data. GIGI-Check detects genotyping errors by using inheritance vectors (IVs), which are inferred by using sparse framework…

RECORD
Desktop

RECORD REcombination Counting and ORDering

Orders loci on genetic linkage maps. RECORD minimizes the total number of…

Orders loci on genetic linkage maps. RECORD minimizes the total number of recombination events. The search algorithm is a heuristic procedure, combining elements of branch-and-bound with local…

MAP
Desktop

MAP Mutation Arranger for defining Phenotype-related SNV

A user-friendly program with multiple functions that supports the determination…

A user-friendly program with multiple functions that supports the determination of recurrent or phenotype-specific mutations and provides graphic illustration images to the users. Its operation…

Loki
Desktop

Loki

Monte Carlo analysis of multiple QTL. Loki can be used to perform multipoint…

Monte Carlo analysis of multiple QTL. Loki can be used to perform multipoint linkage and segregation analysis of quantitative traits on large pedigrees. Comparisons between the nuclear family and…

GADS
Desktop

GADS

A software tool for the multipoint parametric linkage analysis of quantitative…

A software tool for the multipoint parametric linkage analysis of quantitative traits distributed with a spike. The software may be applied to large pedigrees, including thousands of members. The…

Multiple TDT
Desktop

Multiple TDT Multiple Transmission/Disequilibrium Tests

Allows users to perform a Transmission/disequilibrium (TDT) test by using…

Allows users to perform a Transmission/disequilibrium (TDT) test by using multiple close-linked markers. Multiple TDT is a statistical method to analyze multiple tightly linked markers and multisite…

ABT
Dataset

ABT Alfalfa Breeder's Toolbox

Provides a repository dedicated to alfalfa. ABT is a platform gathering…

Provides a repository dedicated to alfalfa. ABT is a platform gathering information about sequencing and assembling of the alfalfa genome derived from a diploid and a tetraploid. It includes a wide…

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