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http://www.icr.ac.uk/cancgen/molgen/MolPopGen_Bioinformatics.htm

Software application for multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal. SNPLINK requires these other programs installed on the system: MERLIN (used for nonparametric analysis), ALLEGRO (used for parametric analysis), R and PERL, all are freely available. (entry from Genetic Analysis Software)

Proper citation: SNPLINK (RRID:SCR_009403) Copy   

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http://orclinux.creighton.edu/snpp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. A dynamic general database management system to manage high-throughput SNP genotyping data. It provides several functions, including data importing with comparison, Mendelian inheritance check within pedigrees, data compiling and exporting. Furthermore, SNPP may generate files for repeat genotyping and transform them into files that can be executed by a liquid handling system.

Proper citation: SNPP (RRID:SCR_009404) Copy   

•   Source: SciCrunch Registry

http://www.maizegenetics.net/tassel

Software package which performs a variety of genetic analyses including association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information. These new analyses should permit association analysis in a wide range plant and animal species. (entry from Genetic Analysis Software)

Proper citation: TASSEL (RRID:SCR_012837) Copy   

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

Software application (entry from Genetic Analysis Software)

Proper citation: MCLEEPS (RRID:SCR_013062) Copy   

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

Software application (entry from Genetic Analysis Software)

Proper citation: UTIL (RRID:SCR_009424) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 6th,2023. Software package for inferring natural selection from unusual population differentiation between closely related populations. (entry from Genetic Analysis Software)

Proper citation: TREESELECT (RRID:SCR_009422) Copy   

•   Source: SciCrunch Registry

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

Software application that performs permutation testing and computes empirical distributions of order statistics for one and two stage association studies with stratified or unstratified data.

Proper citation: PRESTO: Genetic Association Analysis Software (RRID:SCR_013285) Copy   

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http://genecanvas.ecgene.net/#!index.md#THESIAS:_testing_haplotype_effects_in_association_studies

Software program that performs haplotype-based association analysis in unrelated individuals. This program is based on a maximum likelihood model described in Tregouet et al. 2002 and is linked to the stochastic EM (SEM) algorithm. THESIAS allows the simultaneous estimation of haplotype frequencies and of their associated effects on the phenotype of interest. In its current version, both quantitative and qualitative phenotypes can be studied. Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can be investigated. (entry from Genetic Analysis Software)

Proper citation: THESIAS (RRID:SCR_013449) Copy   

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http://www.dmle.org/

Software application for high-resolution mapping of the position of a disease mutation relative to a set of genetic markers using population linkage disequilibrium (LD). (entry from Genetic Analysis Software)

Proper citation: DMLE (RRID:SCR_013454) Copy   

•   Source: SciCrunch Registry

http://pendientedemigracion.ucm.es/info/prodanim/html/JP_Web.htm

A population genetics computer program that conducts several genetic analyses on multilocus information in a user-friendly environment. Primary functions carried out by MOLKIN are the computation of the between individuals (and populations) molecular coancestry coefficients, the Kinship distance at individual and population levels. Additionally, users can compute with MOLKIN a set of among populations, genetic distances and F statistics from multilocus information. The program will help researchers or those responsible for population management to assess genetic variability and population structure at reduced costs with respect to dataset preparation (entry from Genetic Analysis Software)

Proper citation: MOLKIN (RRID:SCR_013262) Copy   

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http://www.bios.unc.edu/~lin/hapstat/

Software interface for the statistical analysis of haplotype-disease association. HAPSTAT allows the user to estimate or test haplotype effects and haplotype-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty and study design. The current version considers cross-sectional, case-control and cohort studies. (entry from Genetic Analysis Software)

Proper citation: HAPSTAT (RRID:SCR_013382) Copy   

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

Software application that implements a novel variable selection method for GWAS data and is able to handle more than half million SNPs. Extensive simulation studies and real data analysis show that this method enjoys high power and low false discovery rate compared to existing variable selection methods. The variables selected by GWASelect can be readily placed into a logistic regression model for disease prediction. The current release is designed for binary outcome under the additive mode of inheritance. (entry from Genetic Analysis Software)

Proper citation: GWASELECT (RRID:SCR_013303) Copy   

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http://www.biostat.ucsf.edu/sen/rqtldesign.html

Software application to help plan quantitative trait locus (QTL) experiments. (entry from Genetic Analysis Software)

Proper citation: R/QTLDESIGN (RRID:SCR_013424) Copy   

•   Source: SciCrunch Registry

http://snippeep.sourceforge.net/

Software application that is an interactive graphic interface to visualise results from whole genome genotyping. It allows one to visualise single subjects and groups of subjects, and provides a direct connection with the UCSC Genome Browser. (entry from Genetic Analysis Software)

Proper citation: SNIPPEEP (RRID:SCR_013309) Copy   

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http://csg.sph.umich.edu//abecasis/QTDT/

Software application that performs linkage disequilibrium (TDT) and association analysis for quantitative traits. Includes support for the methods of Abecasis et al. (2000), Fulker et al. (1999), Monks et al. (1998), Allison (TDTQ5, 1997) and Rabinowitz (1997). Supports families of any size, with or without parental information. Includes simple variance components modelling. Interfaces with SimWalk2 for IBD estimation. (entry from Genetic Analysis Software)

Proper citation: QTDT (RRID:SCR_013391) Copy   

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http://www.reading.ac.uk/Statistics/genetics/software.html

Software application for Bayesian estimation of the coancestry coefficient FST (entry from Genetic Analysis Software)

Proper citation: BAYESFST (RRID:SCR_013479) Copy   

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

Software programs for pedigree analysis, including segregation analysis, gene extinction, and pedigree graphics. (entry from Genetic Analysis Software)

Proper citation: PEDPACK (RRID:SCR_013125) Copy   

•   Source: SciCrunch Registry

http://bioinfo.cs.technion.ac.il/superlink/

Software program that performs exact linkage analysis with the same input-output relationships as in standard genetic linkage programs such as LINKAGE, FASTLINK, VITESSE, but can run larger files than previous programs. (entry from Genetic Analysis Software)

Proper citation: SUPERLINK (RRID:SCR_013360) Copy   

•   Source: SciCrunch Registry

http://www.reading.ac.uk/Statistics/genetics/software.html

Software application for Bayesian estimation of the population inbreeding coefficient f (entry from Genetic Analysis Software)

Proper citation: HWMET (RRID:SCR_013480) Copy   

•   Source: SciCrunch Registry

http://pga.gs.washington.edu/VH1.html

Software application for displaying estimated haplotype data (entry from Genetic Analysis Software)

Proper citation: VH (RRID:SCR_013402) Copy   

•   Source: SciCrunch Registry