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https://cran.r-project.org/web/packages/adegenet/index.html

Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)

Proper citation: ADEGENET (RRID:SCR_000825) Copy   

•   Source: SciCrunch Registry

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

Software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can * phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. * infer sporadic missing genotype data. * impute ungenotyped markers that have been genotyped in a reference panel. * perform single marker and haplotypic association analysis. * detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals. Beagle can also be used in conjunction with PRESTO, a program for fast and flexible permutation testing. PRESTO can compute empirical distributions of order statistics, analyze stratified data, and determine significance levels for one-stage and two-stage genetic association studies. BEAGLE is written in Java and runs on any computing platform with a Java version 1.6 interpreter (e.g. Windows, Unix, Linux, Solaris, Mac).

Proper citation: BEAGLE (RRID:SCR_001789) Copy   

•   Source: SciCrunch Registry

http://www.math.hkbu.edu.hk/~mng/CLUSTAG/CLUSTAG.html

Software application that uses hierarchical clustering and graph methods for selecting tag SNPs (single nucleotide polymorphisms). Cluster and set-cover algorithms are developed to obtain a set of tag SNPs that can represent all the known SNPs in a chromosomal region, subject to the constraint that all SNPs must have a squared correlation R2 > C with at least one tag SNP, where C is specified by the user. The program is implemented with Java, and it can run in Windows platform as well as the Unix environment.

Proper citation: CLUSTAG (RRID:SCR_001816) Copy   

•   Source: SciCrunch Registry

http://research.i2r.a-star.edu.sg:8080/kleisli/demos/pedigree/

Software application (entry from Genetic Analysis Software)

Proper citation: PEDIGREE-VISUALIZER (RRID:SCR_000842) Copy   

•   Source: SciCrunch Registry

http://vorlon.case.edu/~jxl175/haplotyping.html

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. Software application for inferring haplotypes from genotypes on pedigree data (entry from Genetic Analysis Software)

Proper citation: PEDPHASE (RRID:SCR_000843) Copy   

•   Source: SciCrunch Registry

http://animalgene.umn.edu/locusmap/index.html

Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software)

Proper citation: LOCUSMAP (RRID:SCR_000840) Copy   

•   Source: SciCrunch Registry

http://www-genome.wi.mit.edu/ftp/pub/software/rhmapper/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. An interactive software program for radiation hybrid mapping (entry from Genetic Analysis Software)

Proper citation: RHMAPPER (RRID:SCR_000845) Copy   

•   Source: SciCrunch Registry

http://www.people.fas.harvard.edu/~junliu/genotype/

Software application (entry from Genetic Analysis Software)

Proper citation: GS-EM (RRID:SCR_003992) Copy   

•   Source: SciCrunch Registry

http://gaow.github.io/genetic-analysis-software/l-1.html#ldsupport

Software application (entry from Genetic Analysis Software)

Proper citation: LDSUPPORT (RRID:SCR_007036) Copy   

•   Source: SciCrunch Registry

https://www.jurgott.org/linkage/LinkagePC.html

Standard software package for genetic linkage called LINKAGE. Genetic linkage analysis is statistical technique used to map genes and find approximate location of disease genes.

Proper citation: LINKAGE (RRID:SCR_007033) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/abecasis/GOLD/

Software package that provides a graphical summary of linkage disequilibrium in human genetic data. The graphical summary is well suited to the analysis of dense genetic maps, where contingency tables are cumbersome to interpret. An interface to the Simwalk2 application allows for the analysis of family data.

Proper citation: Graphical Overview of Linkage Disequilibrium (RRID:SCR_007151) Copy   

•   Source: SciCrunch Registry

http://gaow.github.io/genetic-analysis-software/l/linkage---ceph/

Software application (entry from Genetic Analysis Software)

Proper citation: LINKAGE - CEPH (RRID:SCR_007048) Copy   

•   Source: SciCrunch Registry

http://compgen.rutgers.edu/multimap.shtml

Software program for automated construction of genetic maps (entry from Genetic Analysis Software)

Proper citation: MULTIMAP (RRID:SCR_007168) Copy   

•   Source: SciCrunch Registry

http://www.uni-bonn.de/~umt70e/soft.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application that calculates the sample size required for obtaining a prescribed power against a specified alternative for TDT. (entry from Genetic Analysis Software)

Proper citation: TDTPOWER (RRID:SCR_005021) Copy   

•   Source: SciCrunch Registry

http://www.stat.washington.edu/thompson/Genepi/MORGAN/Morgan.shtml

Software programs for segregation and linkage analysis, using a variety of Markov chain Monte Carlo (MCMC) methods. Includes MCMC methods for multilocus gene identity by descent (including homozygosity mapping) and Monte Carlo Lod scores. Also, other programs for EM analysis of quantitative traits.

Proper citation: MORGAN (RRID:SCR_006906) Copy   

•   Source: SciCrunch Registry

http://darwin.uvigo.es/software/treescan.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software application that is intended to provide p-values for the hypothesis of association between evolutionary clades and continuous traits, using haplotype trees. (entry from Genetic Analysis Software)

Proper citation: TREESCAN (RRID:SCR_007108) Copy   

•   Source: SciCrunch Registry

http://pngu.mgh.harvard.edu/purcell/whap/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 24, 2015. This package is no longer supported. The majority of the functionality for conditional haplotype tests in population-based samples has been implemented in PLINK, with a better interface and more robust, faster computation: please use that from now on. Software tool to perform haplotype-based association analysis, for quantitative and qualitative traits, in population and family samples, using single nucleotide polymorphism or multiallelic marker data. What whap can do: * Analyze quantitative and qualitative traits * Handle unrelated individuals and/or parent-offspring trio data * Perform a regression-based haplotype association test for SNP data * Perform a secondary test based on pairwise haplotype similarity * Phase genotype data using a standard E-M approach, and handle ambiguity in E-M inferred haplotypes * Include covariates and moderator variables * Flexibly constrain effects across haplotypes to tested nested models * Perform a robust within-family test when parental genotypes are present * Analyze multiallelic markers (new) * Use dominant or recessive (new) genetic models (new)

Proper citation: Whap (RRID:SCR_007103) Copy   

•   Source: SciCrunch Registry

http://genetics.agrsci.dk/~bg/popgen/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software application that calculates a number of different genetic identities, phylogeny reconstructing measures, and distance reconstructing measures (entry from Genetic Analysis Software)

Proper citation: POPDIST (RRID:SCR_004904) Copy   

•   Source: SciCrunch Registry

http://www.geneticepi.com/Research/software/software.html

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

Proper citation: MILD (RRID:SCR_003335) Copy   

•   Source: SciCrunch Registry

http://linkage.rockefeller.edu/pawe3d/

Software application (entry from Genetic Analysis Software)

Proper citation: PAWE-3D (RRID:SCR_003326) Copy   

•   Source: SciCrunch Registry