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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
http://www.flintbox.com/public/project/500/
Software application to generate visual patterns that can be easily interpreted as a single specific Single Nucleotide Polymorphism (SNP) genotype, based on reiterative pattern recognition from validated SNP data (entry from Genetic Analysis Software)
Proper citation: SNP CHART (RRID:SCR_009386) Copy
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
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
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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