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http://www.joinmap.nl/

Software application for construction of genetic linkage maps for several types of mapping populations: BC1, F2, RILs, (doubled) haploids, outbreeders full-sib family. Can combine (''join'') data derived from several sources into an integrated map. Further: linkage group determination, automatic phase determination for outbreeders full-sib family, several diagnostics, and map charts. Everything available in an intuitive MS-Windows user interface. (entry from Genetic Analysis Software)

Proper citation: JOINMAP (RRID:SCR_009248) Copy   

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https://mathgen.stats.ox.ac.uk/impute/impute.html

Software application for estimating (imputing) unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST. (entry from Genetic Analysis Software)

Proper citation: IMPUTE (RRID:SCR_009245) Copy   

•   Source: SciCrunch Registry

http://chgr.mc.vanderbilt.edu/ritchielab/method.php?method=mdrpdt

Software application (entry from Genetic Analysis Software)

Proper citation: MDR-PDT (RRID:SCR_009243) Copy   

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http://intersnp.meb.uni-bonn.de/

Software application for genome-wide interaction analysis (GWIA) of case-control SNP data. SNPs are selected for joint analysis using a priori information. Sources of information to define meaningful strategies can be statistical evidence (single marker association at a moderate level, computed from the own data) and genetic/biologic relevance (genomic location, function class or pathway information). (entry from Genetic Analysis Software)

Proper citation: INTERSNP (RRID:SCR_009244) Copy   

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http://www.chgb.org.cn/htSNPer/htSNPer.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Java program for characterizing the haplotype block structure and selecting haplotype tagging SNP (entry from Genetic Analysis Software)

Proper citation: HTSNPER (RRID:SCR_009242) Copy   

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http://www.math.mtu.edu/~shuzhang/software.html

Software application for testing association using tightly linked markers in nuclear pedigrees (entry from Genetic Analysis Software)

Proper citation: HS-TDT (RRID:SCR_009240) Copy   

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http://www.sanger.ac.uk/resources/software/margarita/

Software application that infers genealogies from population genotype data and uses these to map disease loci. These genealogies take the form of the Ancestral Recombination Graph (ARG). The ARG defines a genealogical tree for each locus, and as one moves along the chromosome the topologies of consecutive trees shift according to the impact of historical recombination events. (entry from Genetic Analysis Software)

Proper citation: MARGARITA (RRID:SCR_009279) Copy   

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http://www.dpw.wau.nl/pv/PUB/MapComp/

Software application that can be used to compare linkage maps obtained from different sources/populations/etc.. It will draw the linkage maps and look for common marker names, these are then connected in the drawing with dashed lines. All neighboring maps are compared in this way. Images can be printed and saved. Orders of the MAPs (ie which map is compared with which other map) can be changed and maps can be flipped (right mouse button). remark: MapComp bears close relationships with the GGT software package (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MAPINSPECT (RRID:SCR_009277) Copy   

•   Source: SciCrunch Registry

http://mapdisto.free.fr/

Software program for mapping genetic markers in experimental segregating populations like backcross, doubled haploids, single-seed descent. Its specificity is to propose recombination fraction estimates in case of segregation distortion. It can (1) compute and draw genetic maps easily and quickly through a graphical interface; (2) facilitate the analysis of marker data showing segregation distortion due to differential viability of gametes or zygotes. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MAPDISTO (RRID:SCR_009275) Copy   

•   Source: SciCrunch Registry

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

Software application for multiple pairwise linkage analysis under interference (entry from Genetic Analysis Software)

Proper citation: MAP/MAP+/MAP+H/MAP2000 (RRID:SCR_009272) Copy   

•   Source: SciCrunch Registry

http://www.marksgeneticsoftware.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that tests for population structure through the use of Mantel tests (entry from Genetic Analysis Software)

Proper citation: MANTEL-STRUCT (RRID:SCR_009271) Copy   

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http://pritch.bsd.uchicago.edu/software/maldsoft_download.html

Software program for admixture mapping of complex trait loci, using case-control data. The samples should come from a recently-admixed population; additional ''learning'' samples from the parental populations are helpful. (entry from Genetic Analysis Software)

Proper citation: MALDSOFT (RRID:SCR_009269) Copy   

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http://ftp://linkage.rockefeller.edu/software/lrtae/

Software application to compute a likelihood ratio test statistic that increases power to detect genetic association in the presence of phenotype, genotype, and/or haplotype misclassification errors. In addition, the program produces asymptotically unbiased estimates of frequency parameters. (entry from Genetic Analysis Software)

Proper citation: LRTAE (RRID:SCR_009265) Copy   

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http://c2s2.yale.edu/software/lot/

Software application (entry from Genetic Analysis Software)

Proper citation: LOT (RRID:SCR_009261) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/genomic_control/genomic_control.htm

Software application where GC implements the genomic control models. GCF implements the basic Genomic Control approach, but adjusts the p-values for uncertainty in the estimated effect of substructure. This approach is preferable if a large number of tests will be evaluated because it provides a more accurrate assessment of the significance level for small p-values. (entry from Genetic Analysis Software)

Proper citation: GC/GCF (RRID:SCR_009075) Copy   

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http://wpicr.wpic.pitt.edu/WPICCompGen/newcovibd/covibd.htm

Software application that refines linkage analysis of affected sibpairs by considering attributes or environmental exposures thought to affect disease liability. This refinement utilizes a mixture model in which a disease mutation segregates in only a fraction of the sibships, with the rest of the sibships unlinked. Covariate information is used to predict membership within the two groups corresponding to the linked and unlinked sibships. The pre-clustering model uses covariate information to first form two probabilistic clusters and then tests for excess IBD-sharing in the clusters. The Cov-IBD model determines probabilistic group membership by joint consideration of covariate and IBD values. (entry from Genetic Analysis Software)

Proper citation: COVIBD (RRID:SCR_009155) Copy   

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http://chgr.mc.vanderbilt.edu/page/gist

Software package to test if a marker can account in part for the linkage signal in its region. There are two versions of the software: Windows and Linux/Unix.

Proper citation: Genotype-IBD Sharing Test (RRID:SCR_006257) Copy   

•   Source: SciCrunch Registry

http://www003.upp.so-net.ne.jp/pub/publications.html#sl

Software application for inkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs. (entry from Genetic Analysis Software)

Proper citation: LDGROUP (RRID:SCR_006282) Copy   

•   Source: SciCrunch Registry

http://www.homepages.ed.ac.uk/pmckeigu/pooling/poolscore.htm

Software program for analysis of case-control genetic association studies using allele frequency measurements on DNA pools (entry from Genetic Analysis Software)

Proper citation: POOLSCORE (RRID:SCR_007514) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/blocks.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application aiming at identifying haplotype blocks. The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low. (entry from Genetic Analysis Software)

Proper citation: ENTROPY BLOCKER (RRID:SCR_000123) Copy   

•   Source: SciCrunch Registry