Tools   Select Another Resource Report Type

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://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://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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   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

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

A graphical tool designed for detection of errors in relationship specification in general pedigrees by use of genome scan marker data. (entry from Genetic Analysis Software)

Proper citation: GRR (RRID:SCR_013496) Copy   

•   Source: SciCrunch Registry

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

Software suite of six programs that can be used as a stand-alone extension of the pedigree drawing facilities found in the publicly available version of PEDPACK. (entry from Genetic Analysis Software)

Proper citation: PEDFIDDLER (RRID:SCR_013376) Copy   

•   Source: SciCrunch Registry

http://pga.gs.washington.edu/VG2.html

Software program that presents complete raw datasets of individuals'' genotype data using a display format with samples as rows and polymorphisms as columns. The color code is: (1) blue: homozygous genotype for the common allele; (2) red: heterozygous genotype; (3) yellow: homozygous genotype for the rare allele; and (4) grey: missing data (entry from Genetic Analysis Software)

Proper citation: VG (RRID:SCR_013378) Copy   

•   Source: SciCrunch Registry

http://www.bios.unc.edu/~lin/software/tagIMPUTE/

A command-line program for the imputation of untyped SNPs. tagIMPUTE is based on a few flanking SNPs that can optimally predict the SNP under imputation. (entry from Genetic Analysis Software)

Proper citation: TAGIMPUTE (RRID:SCR_013338) Copy   

•   Source: SciCrunch Registry