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http://www.stat.ohio-state.edu/~statgen/SOFTWARE/SIMPLE/

Software application that calculates linkage statistics, such as lod scores and NPL statistics by Sequential Imputation. (entry from Genetic Analysis Software)

Proper citation: SIMPLE (RRID:SCR_009389) Copy   

•   Source: SciCrunch Registry

http://csg.sph.umich.edu/boehnke/simlink.php

Software program to estimate the probability (power) of detecting linkage given family history information on a set of identified pedigrees. (entry from Genetic Analysis Software)

Proper citation: SIMLINK (RRID:SCR_009387) Copy   

•   Source: SciCrunch Registry

http://dmpi.duke.edu/simla-simulation-software-version-32

SIMulation program that generates data sets of families for use in Linkage and Association studies. It allows the user flexibility in specifying marker and disease placement, locus heterogeneity, disequilibrium between markers and between markers and disease loci. Output is in the form of a LINKAGE pedigree file and is easily utilized, either directly or with minimal reformatting, as input for various genetic analysis packages (entry from Genetic Analysis Software)

Proper citation: SIMLA (RRID:SCR_009385) Copy   

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http://imbs-luebeck.de/imbs/de/node/34

Software application to calculate nominal significance levels and critical LOD scores depending on the length of the investigated region, number of chromosomes, and the cross-over rate. The global significance level as well as the precision of the calculation have to be specified. (entry from Genetic Analysis Software)

Proper citation: SILCLOD (RRID:SCR_009383) Copy   

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http://gaow.github.io/genetic-analysis-software/s-1.html#siberror

Software application that identifies pedigree errors in sibship data. Examples include half siblings, unrelated individuals, identical twins, and parental exclusions. The test statistic is based on the summation of the number of alleles shared by a pair of relatives for a large number of markers and the number of alleles and allele frequencies for those markers. (entry from Genetic Analysis Software)

Proper citation: SIBERROR (RRID:SCR_009380) Copy   

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http://www7.inra.fr/mia/T/MendelSoft/

Software application for identifying all Mendelian inconsistencies in complex pedigree data with thousand of individuals, including many loops and several errors. Can also infer missing genotypes. (entry from Genetic Analysis Software)

Proper citation: MENDELSOFT (RRID:SCR_013177) Copy   

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http://dlin.web.unc.edu/software/spreg-2/

Software program for performing regression analysis of secondary phenotype data in case-control association studies. Secondary phenotypes are quantitative or qualitative traits other than the case-control status. Because the case-control sample is not a random sample of the general population, standard statistical analysis of secondary phenotype data can yield very misleading results. SPREG implements valid and efficient statistical methods. (entry from Genetic Analysis Software)

Proper citation: SPREG (RRID:SCR_013261) Copy   

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https://plant-breeding.uni-hohenheim.de/software.html#jfmulticontent_c110647-2

Software application (entry from Genetic Analysis Software)

Proper citation: PLABQTL (RRID:SCR_012789) Copy   

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http://econpapers.repec.org/software/bocbocode/s438902.htm

Software application (entry from Genetic Analysis Software)

Proper citation: HAPBLOCK 2 (RRID:SCR_012788) Copy   

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https://www.dkfz.de/en/epidemiologie-krebserkrankungen/software/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May24,2023. Software program that implements the Mantel statistics as proposed by Beckmann et al. (2005) to test for association between genetic markers and phenotypes in case-control studies using haplotype information. The potential value of haplotypes has attracted widespread interest in the mapping of complex traits. Haplotype sharing methods take into account linkage disequilibrium information between multiple markers, and may have good power to detect predisposing genes. We present a new approach based on Mantel statistics for space time clustering, which we developed in order to improve the power of haplotype sharing analysis for gene mapping in complex disease. The new statistic correlates genetic similarity and phenotypic similarity across pairs of haplotypes for case-only and case-control studies. The genetic similarity is measured as the shared length between haplotypes around a putative disease locus. Alternative measures for the phenotypic similarity were implemented. (entry from Genetic Analysis Software)

Proper citation: TOMCAT (RRID:SCR_013120) Copy   

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http://cuke.hort.ncsu.edu/cucurbit/wehner/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program to estimate genetic effects and heritabilities of quantitative traits in breeding populations consisting of six related generations (entry from Genetic Analysis Software)

Proper citation: SASQUANT (RRID:SCR_013122) Copy   

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http://dlin.web.unc.edu/software/SCORE-Seq/

A command-line program for detecting disease associations with rare variants in sequencing studies. The mutation information is aggregated across multiple variant sites of a gene through a weighted linear combination and then related to disease phenotypes through appropriate regression models. The weights can be constant or dependent on allele frequencies and phenotypes. The association testing is based on score-type statistics. The allele-frequency threshold can be fixed or variable. Statistical significance can be assessed by using asymptotic normal approximation or resampling. The current release covers binary and continuous traits with arbitrary covariates under case-control and cross-sectional sampling. (entry from Genetic Analysis Software)

Proper citation: SCORE-SEQ (RRID:SCR_013121) Copy   

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http://www.aps.uoguelph.ca/~msargol/qmsim/

Software application designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data. (entry from Genetic Analysis Software)

Proper citation: QMSIM (RRID:SCR_013123) Copy   

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http://www.stat.washington.edu/thompson/Genepi/InSegT.shtml

Software application that constructs feasible haplotype configurations and the corresponding segregation types on pedigrees. the haplotype configuration minimizes recombinations on the pedigree. (entry from Genetic Analysis Software)

Proper citation: INSEGT (RRID:SCR_013126) Copy   

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

Software application that is a GLF-based variant caller for next-generation sequencing data. It takes one/three/multiple GLF format genotype likelihood files as input and generates a VCF-format set of variant calls as output. (entry from Genetic Analysis Software)

Proper citation: GLFSINGLE/GLFTRIO/GLFMULTIPLES (RRID:SCR_013128) Copy   

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https://sourceforge.net/projects/ggsd/

Web-based, relational database driven data management software package for the management of large scale genetic studies. (entry from Genetic Analysis Software)

Proper citation: GGSD (RRID:SCR_013129) Copy   

•   Source: SciCrunch Registry

http://www.som.soton.ac.uk/research/geneticsdiv/epidemiology/chromscan/

A statistical based program for association mapping of disease genes. It utilises the Malecot model and the linkage disequilibrium (LD) map for the candidate region to analyse the genotypes derive from large sample of matched cases and controls. (entry from Genetic Analysis Software)

Proper citation: CHROMSCAN (RRID:SCR_013131) Copy   

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http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application to compute composite measures of linkage disequilibrium, their variances and covariances, and statistical tests, for all pairs of alleles from two loci when linkage phase is unkown. An extension of Weir and Cockerham (1989) to apply to multi-allelic loci. (entry from Genetic Analysis Software)

Proper citation: COMPOSITELD (RRID:SCR_013132) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/eathomp/Anonftp/PANGAEA/BOREL/

Software application for inference of genealogical relationships from genetic data, including sibship inference.

Proper citation: BOREL (RRID:SCR_013135) Copy   

•   Source: SciCrunch Registry

http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application for statistical methods for disease and genetic marker associations using cases and their parents. These methods include an extension of the transmission/disequilibrium test (TDT) for multiple marker alleles, as well as additional general tests sensitive to associations that depend on dominant or recessive genetic mechanisms. (entry from Genetic Analysis Software)

Proper citation: GASSOC (RRID:SCR_013136) Copy   

•   Source: SciCrunch Registry