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https://gmod.org/wiki/CMap.1

Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software)

Proper citation: CMAP (RRID:SCR_009034) Copy   

•   Source: SciCrunch Registry

http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/LDMAP

Software program for constructing linkage disequilibrium (LD) maps. (entry from Genetic Analysis Software)

Proper citation: LDMAP (RRID:SCR_006308) Copy   

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http://www-rcf.usc.edu/~gqian/software.htm (not available)

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)

Proper citation: MRH (RRID:SCR_000841) Copy   

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http://wwwchg.duhs.duke.edu/research/osa.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software application that allows the researcher to evaluate evidence for linkage even when heterogeneity is present in a data set. This is not an unusual occurrence when studying diseases of complex origin. Families are ranked by covariate values in order to test evidence for linkage among homogeneous subsets of families. Because families are ranked, a priori covariate cutpoints are not necessary. Covariates may include linkage evidence at other genes, environmental exposures, or biological trait values such as cholesterol, age at onset, and so on.

Proper citation: OSA (RRID:SCR_002016) Copy   

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http://faculty.washington.edu/browning/presto/presto.html

Software application that performs permutation testing and computes empirical distributions of order statistics for one and two stage association studies with stratified or unstratified data.

Proper citation: PRESTO: Genetic Association Analysis Software (RRID:SCR_013285) Copy   

•   Source: SciCrunch Registry

http://csg.sph.umich.edu//abecasis/QTDT/

Software application that performs linkage disequilibrium (TDT) and association analysis for quantitative traits. Includes support for the methods of Abecasis et al. (2000), Fulker et al. (1999), Monks et al. (1998), Allison (TDTQ5, 1997) and Rabinowitz (1997). Supports families of any size, with or without parental information. Includes simple variance components modelling. Interfaces with SimWalk2 for IBD estimation. (entry from Genetic Analysis Software)

Proper citation: QTDT (RRID:SCR_013391) Copy   

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https://dsgweb.wustl.edu/aldi/software/manuals/unphased/Unphased_manual.pdf

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A suite of programs for association analysis of multilocus haplotypes from unphased genotype data. These include TDTPHASE for case-parent trios, COCAPHASE for case/control data, QTPHASE for quantitative traits in unrelateds, PDTPHASE for general pedigrees, and QPDTPHASE for quantitative traits in general pedigrees. Features include global and individual haplotype tests, main effects and conditional tests, grouping of rare haplotypes, pairwise comparisons of haplotype risk, flexible permutation procedures and calculation of LD measures.

Proper citation: UNPHASED (RRID:SCR_009056) Copy   

•   Source: SciCrunch Registry

http://www.inra.fr/mia/T/CarthaGene/

A genetic/radiation hybrid mapping software that looks for multiple populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood estimation and powerful ordering algorithms inspired from TSP (Traveling Salesman Problem) technology. It can handle large data sets made up of different populations (either F2 backcross, recombinant inbred lines, F2 intercross, phase known outbreds, haploid/diploid radiation hybrids). It can also exploit existing syntenic relationships between the organism mapped and a reference (sequenced) organism for accurate dense RH mapping. (entry from Genetic Analysis Software)

Proper citation: CARTHAGENE (RRID:SCR_009013) Copy   

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http://www.sph.umich.edu/csg/liang/genome/

Software application to simulate sequences drawn from a population under the Wright-Fisher neutral model. The purpose of this program is to simulate sequences on the whole genome scale within practical time. (entry from Genetic Analysis Software)

Proper citation: GENOME (RRID:SCR_008949) Copy   

•   Source: SciCrunch Registry

http://www.biostat.harvard.edu/~fbat/fbat.htm

Software application that allows the user to test for association/linkage between disease phenotypes and haplotypes by utilizing family-based controls. The method extends the approach for testing described in Rabinowitz and Laird (2000) to handle multiple tightly linked markers. It is robust to population admixture, yet efficient in the sense that it utilizes data from families where phase cannot be completely resolved in all individuals by using weights, which are estimated from the sample. However, the method remains robust to population stratification and population admixture. The method can handle any type of phenotype, including multiple phenotypes and missing parents, marker data, and/or phase, and provides both bi-allelic and multi-allelic tests. PowerFBAT is a tool for power simulation of association analysis using FBAT with binary outcomes. XWXW is an extension to the Haseman-Elston method for non-parametric linkage test with quantitative traits. XDT is a software that performs classical TDT, SDT and Rabinowitz TDT for nuclear families (not supported anymore). (entry from Genetic Analysis Software)

Proper citation: FBAT (RRID:SCR_009178) Copy   

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http://galton.uchicago.edu/~mcpeek/software/dhsmap/

Software application for fine-mapping of qualitative traits by linkage disequilibrium. Given a set of marker haplotypes or genotypes from affected individuals, haplotypes or genotypes from appropriately selected controls, and a genetic map of the markers at which both sets of individuals are typed, DHSMAP estimates the location of the trait-associated variant by maximum likelihood or maximum quasi-likelihood. (entry from Genetic Analysis Software)

Proper citation: DHSMAP (RRID:SCR_009160) Copy   

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http://pritch.bsd.uchicago.edu/treeld.html

Free software tool for mapping complex trait loci. TreeLD performs a multipoint LD-analysis by inferring the ancestry of a genomic region and analyzing this ancestry for signals of disease mutations. The generated likelihoods can be used to test for the presence of a disease locus and to fine-map its location, providing a point estimate and a credible region. Furthermore, the package provides a novel way of visualizing the association signal in a sample. TreeLD is designed for high-density SNP haplotypes and can be applied to case-control data, TDT trio data and quantitative trait data. (entry from Genetic Analysis Software)

Proper citation: TREELD (RRID:SCR_009111) Copy   

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http://pritchardlab.stanford.edu/software.html

Software application that is a companion program to STRUCTURE that is a structured association method, for use in association mapping, enabling valid case-control studies even in the presence of population structure. (entry from Genetic Analysis Software)

Proper citation: STRAT (RRID:SCR_009110) Copy   

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http://www.molecular-haplotype.org/finesse/finesse_intro.htm

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application to incorporate regressive models into the VITESSE likelihood engine.

Proper citation: FINESSE (RRID:SCR_009100) Copy   

•   Source: SciCrunch Registry

http://dmpi.duke.edu/apl-osa-beta-version

Software application that in the presence of genetic heterogeneity, can identify a genetically homogenous subset of families based on a trait-related covariate. APL-OSA then tests the relationship between the association statistics (i.e., the APL statistics) calculated based on the subset and the family-specific covariate. APL-OSA is based on the OSA method for linkage and the family-based association test, APL. Thus, APL-OSA has similar properties with OSA and APL. Bi-alleleic markers such as SNPs are accepted by APL-OSA. APL-OSA is a single-marker test and considers one covariate each time. (entry from Genetic Analysis Software)

Proper citation: APL-OSA (RRID:SCR_009124) Copy   

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http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.

Proper citation: EHPLUS (RRID:SCR_009159) Copy   

•   Source: SciCrunch Registry

https://academic.oup.com/bioinformatics/article/21/24/4430/180359

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 7,2025. Software application that is a rank-based meta-analysis method for analyzing results from genome-wide linkage searches. A software package is now available. The gsma software calculates the summed rank for any number of studies and bins, then obtains p-values for the Summed Rank and the Ordered Rank statistics, by simulation. Weighted and unweighted analyses are performed. A test data set is included. (entry from Genetic Analysis Software)

Proper citation: GSMA (RRID:SCR_009214) Copy   

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https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-imprinting/index.html

Software application that is a modification of the GENEHUNTER software package (version 1.3)that allows users to perform parametric (LOD-score) analysis of traits caused by imprinted genes - that is, of traits showing a parent-of-origin effect. (entry from Genetic Analysis Software)

Proper citation: GENEHUNTER-IMPRINTING (RRID:SCR_009192) Copy   

•   Source: SciCrunch Registry

http://bioinfo.cs.technion.ac.il/haploblock/

Software package which provides an integrated approach to haplotype block identification, haplotype resolution and linkage disequilibrium mapping, suitable for high-density phased or unphased SNP data. (entry from Genetic Analysis Software)

Proper citation: HAPLOBLOCK (RRID:SCR_009223) Copy   

•   Source: SciCrunch Registry

http://www-hto.usc.edu/msms/HapBlock/

Software application (entry from Genetic Analysis Software)

Proper citation: HAPBLOCK (RRID:SCR_009220) Copy   

•   Source: SciCrunch Registry