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…
Desktop app
Sequential Oligogenic… Sequential Oligogenic Linkage Analysis Routines

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…

Desktop app
Linkage and… Linkage and Association Modeling in Pedigrees

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…

Desktop app
SimWalk2 SimWalk2

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…

Desktop app
Mendel Mendel

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…

Desktop app
Pedigree… Pedigree Reconstruction and Identification of a…

PRIMUS Pedigree Reconstruction and Identification of a Maximum Unrelated Set

A pedigree reconstruction algorithm that uses estimates of genome-wide identity…

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…

Desktop app
Lep-MAP Lep-MAP

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…

Desktop app
GADS GADS

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…

Desktop app
solarius solarius

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…

Desktop app
Rare-variant… Rare-variant Pedigree-based Simulator

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…

Desktop app
TLINKAGE TLINKAGE

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…

Desktop app
Vitesse Vitesse

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.

Desktop app
SEQLinkage SEQLinkage

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…

Desktop app
Web app
Superlink-Online SNP Superlink-Online SNP

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…

Desktop app
ExomePicks ExomePicks

ExomePicks

Suggests individuals to be sequenced in a large pedigree. ExomePicks assumes…

Suggests individuals to be sequenced in a large pedigree. ExomePicks assumes that a genotyping chip or another cost effective means will be used to determine IBD sharing in the pedigree and that,…

Desktop app
Loki Loki

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…

Desktop app
Merlin Merlin

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…

Desktop app
PedCheck PedCheck

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…

Desktop app
PSEUDOMARKER PSEUDOMARKER

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…

Desktop app
easyLINKAGE easyLINKAGE

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…

Desktop app
GeneHunter GeneHunter

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…

Desktop app
GIGI-Check GIGI-Check

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…

Desktop app
GIGI-Pick GIGI-Pick

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…

Desktop app
Allegro Deprecated Allegro

Allegro

A computer program for multipoint genetic linkage analysis and related…

A computer program for multipoint genetic linkage analysis and related calculations. Allegro can do both classical parametric linkage analysis and analysis based on allele sharing models. In…

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