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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

Proper citation: LOT (RRID:SCR_009261) Copy   

•   Source: SciCrunch Registry

http://www.uoguelph.ca/~rdanzman/software/PROBMAX/

Software application for assigning unknown parentage in pedigree analysis from known genotypic pools of parents and progeny (entry from Genetic Analysis Software)

Proper citation: PROBMAX (RRID:SCR_009337) Copy   

•   Source: SciCrunch Registry

http://www.statgen.ucr.edu/software.html

Software application that is a user defined SAS procedure for mapping quantitative trait loci (QTL). Since this procedure is not a built-in SAS procedure, users need to obtain a copy of the executable file of PROC QTL and install the software in their personal computers before PROC QTL can be executed. Of course, users need a regular SAS license prior to the installation of PROC QTL. Once PROC QTL is installed, it can be called just like any other SAS procedures. Users will not notice the differences between this customized procedure and other built-in SAS procedures. (entry from Genetic Analysis Software)

Proper citation: PROC QTL (RRID:SCR_009338) Copy   

•   Source: SciCrunch Registry

http://phg.mc.vanderbilt.edu/content/powertrim

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11,2023. Software application that automate the decision to remove objects from a pedigree with a minimum loss information (entry from Genetic Analysis Software)

Proper citation: POWERTRIM (RRID:SCR_009333) Copy   

•   Source: SciCrunch Registry

http://ftp://statgen.ncsu.edu/pub/zaykin/

Software application performing a shuffling version of the exact conditional tests for different combinations of allelic and genotypic disequilibrium on haploid and diploid data, or their combination. (entry from Genetic Analysis Software)

Proper citation: MLD (RRID:SCR_009298) Copy   

•   Source: SciCrunch Registry

http://ftp://ftp.biomath.jussieu.fr/pub/mlbgh (not available)

Software application that is an extension of the GENEHUNTER program to perform sib-pair and sib-ship linkage analysis using the Maximum Likelihood Binomial (MLB) method. (entry from Genetic Analysis Software)

Proper citation: MLBGH (RRID:SCR_009297) Copy   

•   Source: SciCrunch Registry

http://mga.bionet.nsc.ru/soft/mitpene/mitpene.html (in Russian)

Software program for analysis of mitochondrial diseases (entry from Genetic Analysis Software)

Proper citation: MITPENE (RRID:SCR_009294) Copy   

•   Source: SciCrunch Registry

http://www.uni-kiel.de/medinfo/mitarbeiter/krawczak/download/index.html

Software application (entry from Genetic Analysis Software)

Proper citation: MKGST (RRID:SCR_009295) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/Minimac

Software application that is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation. (entry from Genetic Analysis Software)

Proper citation: MINIMAC (RRID:SCR_009292) Copy   

•   Source: SciCrunch Registry

http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application (entry from Genetic Analysis Software)

Proper citation: MFLINK (RRID:SCR_009290) Copy   

•   Source: SciCrunch Registry