Tools   Select Another Resource Report Type

http://www.hsph.harvard.edu/faculty/alkes-price/software/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. A software suite designed to more powerfully leverage clinical-covariates such as age, bmi, smoking status, and gender when conducting case-control association studies. Including these covariates in standard regression models is not only suboptimal, but can in many instances reduce power. LTSOFT employs a liability threshold model approach that takes advantage of known epidemiological results to better model the covariates'' relationship to the phenotype of interest (entry from Genetic Analysis Software)

Proper citation: LTSOFT (RRID:SCR_009266) Copy   

•   Source: SciCrunch Registry
  

https://github.com/gaow/genetic-analysis-software/blob/master/pages/LRP.md

Software application that is part of the LINKAGE auxiliary program (entry from Genetic Analysis Software)

Proper citation: LRP (RRID:SCR_009263) Copy   

•   Source: SciCrunch Registry
  

http://www.gohad.uwa.edu.au/software/simhap

Software application providing a comprehensive modelling framework and a multiple-imputation approach to haplotypic analysis of population-based data. It uses biallelic SNP genotype data to impute haplotype frequencies at the individual level. SimHap also tests for haplotype associations with outcomes of interest while incorporating the uncertainty around inferred haplotypes into the modelling procedure. SimHap allows epidemiological (ie, non-genetic) and both single SNP and haplotype association analyses of quantitative Normal, binary, longitudinal and right-censored outcomes under a range of genetic models. SimHap can accommodate large data sets, and can model genetic and environmental effects, including complex haplotype:environment interactions. SimHap features cross-platform functionality via Java, and a sophisticated graphical user interface (GUI). SimHap will also perform association analysis on more simple epidemiological models, with or without the inclusion of genetic covariates. (entry from Genetic Analysis Software)

Proper citation: SIMHAP (RRID:SCR_009384) Copy   

•   Source: SciCrunch Registry
  

https://genepi.qimr.edu.au/staff/davidD/#sib-pair

Software program that performs a number of simple analyses of family data that tend to be nonparametric or robust in nature, includes IBD and IBS based APM, Haseman-Elston sib pair, TDT and association analyses. (entry from Genetic Analysis Software)

Proper citation: SIB-PAIR (RRID:SCR_009382) Copy   

•   Source: SciCrunch Registry
  

http://statgen.iop.kcl.ac.uk/lpop/

Software application that detects population stratification in samples of unrelated individuals for whom a number of unlinked genotypes have been measured. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: L-POP (RRID:SCR_009262) Copy   

•   Source: SciCrunch Registry
  

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

Software program for analyses a quantitative trait observed on large pedigrees using Markov chain Monte Carlo multipoint linkage and segregation analysis. The trait may be determined by multiple loci. (entry from Genetic Analysis Software)

Proper citation: LOKI (RRID:SCR_009260) Copy   

•   Source: SciCrunch Registry
  

http://dmpi.duke.edu/siblink-v-30

Software application that allows the user to perform multipoint linkage analysis based on estimated IBD sharing between affected sibpairs. IBD sharing is inferred from IBS status, given marker genotypes, frequencies, and locations. Resulting LOD scores are maximized across a grid of possible disease locations and IBD sharing vectors. (entry from Genetic Analysis Software)

Proper citation: SIBLINK (RRID:SCR_009381) Copy   

•   Source: SciCrunch Registry
  

http://alla.cs.gsu.edu/~software/tagging/tagging.html

Software application that can be used for tagging SNP selection and genotype prediction (entry from Genetic Analysis Software)

Proper citation: MLR-TAGGING (RRID:SCR_009299) Copy   

•   Source: SciCrunch Registry
  

http://www.emboss.co.nz/products.php?pid=2

Software application to draw chromosome maps from the output of MAPMAKER/EXP. The output format is a Enhanced Metafile, which can be imported into most Windows-based presentation or document editing programs. (entry from Genetic Analysis Software)

Proper citation: MMDRAWER (RRID:SCR_009296) Copy   

•   Source: SciCrunch Registry
  

http://www.imbs.uni-luebeck.de/pub/minsage/index.html

Software application to calculate the sample size of genotypes minimally required to ensure that all alleles with a specified frequency at one locus are detected with a given confidence (entry from Genetic Analysis Software)

Proper citation: MINSAGE (RRID:SCR_009293) Copy   

•   Source: SciCrunch Registry
  

http://bioinformatics.ust.hk/MegaSNPHunter.html

Software application that takes case-control genotype data as input and produces a ranked list of multi-SNP interactions. In particular, the whole genome is first partitioned into multiple short subgenomes and a boosting tree classifier is built for each subgenomes based on multi-SNP interactions and then used to measure the importance of SNPs. The method keeps relatively more important SNPs from all subgenomes and let them compete with each other in the same way at the next level. The competition terminates when the number of selected SNPs is less than the size of a subgenome. (entry from Genetic Analysis Software)

Proper citation: MEGASNPHUNTER (RRID:SCR_009287) Copy   

•   Source: SciCrunch Registry
  

http://carlit.toulouse.inra.fr/MCQTL/

Software package to perform QTL mapping in multi-cross designs that allows the analysis of the usual populations derived from inbred lines and can link the families by assuming that the QTL locations are the same in all them. Moreover, a diallel modelling of the QTL genotypic effects is allowed in multiple related families. Obviously, the analysis of a single cross is also feasible. (entry from Genetic Analysis Software)

Proper citation: MCQTL (RRID:SCR_009285) Copy   

•   Source: SciCrunch Registry
  

http://www-genome.wi.mit.edu/genome_software

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

Proper citation: MAPMAKER/QTL (RRID:SCR_009283) Copy   

•   Source: SciCrunch Registry
  

http://ib.berkeley.edu/labs/slatkin/eriq/software/mdb_web/

Software application using the mimimum description length model to delineate haplotype blocks (entry from Genetic Analysis Software)

Proper citation: MDBLOCKS (RRID:SCR_009280) Copy   

•   Source: SciCrunch Registry
  

http://www-genepi.med.utah.edu/Genie/

Software application that performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GENIE (RRID:SCR_009197) Copy   

•   Source: SciCrunch Registry
  

http://pngu.mgh.harvard.edu/~purcell/gpc/

Software application for automated power analysis for variance components (VC) quantitative trait locis (QTL) linkage and association tests in sibships, and other common tests (entry from Genetic Analysis Software)

Proper citation: GENETIC POWER CALCULATOR (RRID:SCR_009198) Copy   

•   Source: SciCrunch Registry
  

http://www.daimi.au.dk/~mailund/GeneRecon/

Software application for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position. (entry from Genetic Analysis Software)

Proper citation: GENERECON (RRID:SCR_009195) Copy   

•   Source: SciCrunch Registry
  

http://www.chem.agilent.com/scripts/pds.asp?lpage=34662

A desktop analysis workbench for analyzing high-volume, high-density genotyping data. The software provides a comprehensive set of linkage and association algorithms that allow researchers to discover relationships between genotypes and phenotypes. Researchers can visually explore fully annotated SNPs and genes at varying levels of detail. Designed for biologists and statisticians, GeneSpring GT is capable of importing, visualizing, and analyzing hundreds of thousands of variation measurements simultaneously, for rapid localization of disease or phenotype markers. (entry from Genetic Analysis Software)

Proper citation: GENESPRING GT (RRID:SCR_009196) Copy   

•   Source: SciCrunch Registry
  

http://www.broad.mit.edu/ftp/distribution/software/genehunter/

Software application for multipoint analysis of pedigree data including: non-parametric linkage analysis, LOD-score computation, information-content mapping, haplotype reconstruction (entry from Genetic Analysis Software)

Proper citation: GENEHUNTER (RRID:SCR_009191) Copy   

•   Source: SciCrunch Registry
  

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