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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   

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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   

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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   

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http://www.sapaldia.net/en/

SAPALDIA (Swiss study on Air Pollution and Lung Disease in adults) is a multi-center study in eight geographic areas representing the range of environmental, meteorological and socio-demographic conditions of Switzerland, which studies the effects of air pollution on the respiratory and cardiovascular health in adults. Local centers are: Aarau, Basel, Davos, Geneva, Lugano, Montana, Payerne, and Wald. It was initiated in 1991 (SAPALDIA 1) with a follow-up assessment in 2002 (SAPALDIA 2). This study has allowed to assess 1) prevalence and development of major respiratory and allergic symptoms and diseases and the age-related decline in lung function, 2) the distribution of heart rate variability in the general population over age 50, 3) the association of these health indicators with individual long term exposure to air pollution, other toxic inhalants, life style and molecular factors. Another follow-up examination (SAPALDIA 3) started in January 2010. This study is well positioned to address crucial questions of air pollution epidemiology and important environmental health policy-related questions in the coming years. When SAPALDIA was initiated in 1991, 9''''651 subjects, aged 18 to 60 years, were recruited for a detailed computer-based interview and more than 90% of them underwent lung function and atopy testing. More than 7''''000 of the subjects had bronchial reactivity tested by a methacholine challenge. SAPALDIA shares parts of its study protocol with the European Community Respiratory Health Survey (ECRHS) with which it is linked through the study center of Basel. Since 1991 SAPALDIA has been carefully following address histories of its participants. In the 2002 follow-up, 8''''047 (83%) provided health information, 6''''528 persons underwent physical re-examination, and 6''''345 provided blood samples to establish an extensive blood, plasma, serum and DNA bank. In addition, 1''''813 subjects aged 50 or older participated in 24h-ECG Holter monitoring to provide detailed data on parameters of heart rate variability. With the inclusion of cardiovascular endpoints, SAPALDIA is one of the first studies examining effects from long-term exposure to air pollution on cardiovascular health parameters as well as mutual influence between the respiratory and the cardiovascular system. The SAPALDIA bio-bank has allowed scientific publications on the association between some genetic profiles (gene polymorphism) and the propensity to develop asthma, allergic diseases, or accelerated lung function decline with age. Ongoing studies are focusing on gene-environment interactions a crucial question to understand why some persons suffer more from the effect of air pollution than others.

Proper citation: SAPALDIA (RRID:SCR_013416) Copy   

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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   

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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/pangaea.shtml

Collection of nine software packages for genetic analysis: BOREL, HARDY, MORGAN (now 2 and 3), Pedpack, InSegT, Loki, MCLEEPS, Pedfiddler, and Eclipse.

Proper citation: PANGAEA (RRID:SCR_013119) 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   

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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   

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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 for gene segregation and linkage analysis in breeding population (entry from Genetic Analysis Software)

Proper citation: SASGENE (RRID:SCR_013084) Copy   

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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   

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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   

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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   

•   Source: SciCrunch Registry