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http://stephenslab.uchicago.edu/software.html

Software application (entry from Genetic Analysis Software)

Proper citation: BIMBAM (RRID:SCR_009129) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/ariel/

Software application that explores the effects of rare variants within complex traits through locus-based analysis. There is increasing evidence that rare variants play a role in some complex traits, but their analysis is not straightforward. Locus-based tests become necessary due to low power in rare variant single-point association analyses. In addition, variant quality scores are available for sequencing data, but are rarely taken into account. To enable this analysis, ARIEL has been developed as a locus-wide regression-based collapsing approach that incorporates variant quality scores. (entry from Genetic Analysis Software)

Proper citation: ARIEL (RRID:SCR_009126) Copy   

•   Source: SciCrunch Registry

http://dmpi.duke.edu/apl-osa-beta-version

Software application that in the presence of genetic heterogeneity, can identify a genetically homogenous subset of families based on a trait-related covariate. APL-OSA then tests the relationship between the association statistics (i.e., the APL statistics) calculated based on the subset and the family-specific covariate. APL-OSA is based on the OSA method for linkage and the family-based association test, APL. Thus, APL-OSA has similar properties with OSA and APL. Bi-alleleic markers such as SNPs are accepted by APL-OSA. APL-OSA is a single-marker test and considers one covariate each time. (entry from Genetic Analysis Software)

Proper citation: APL-OSA (RRID:SCR_009124) Copy   

•   Source: SciCrunch Registry

http://watson.hgen.pitt.edu/register/soft_doc.html registration page at: http://watson.hgen.pitt.edu/register

Software application (entry from Genetic Analysis Software)

Proper citation: APM (RRID:SCR_009125) Copy   

•   Source: SciCrunch Registry

http://watson.hgen.pitt.edu/register/soft_doc.html,

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that calculates likelihood on pedigrees (entry from Genetic Analysis Software)

Proper citation: VITESSE (RRID:SCR_009089) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that extends partially observed genotype data to the whole pedigree. Can be used for generating starting points for MCMC samplers and for checking that the genotype data are consistent with the pedigree structure.

Proper citation: APE (RRID:SCR_009122) Copy   

•   Source: SciCrunch Registry

http://ciil.case.edu:3000

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that provides an easy to use web-based user interface to compute individual ancestry estimates using the Maximum Likelihood Estimation method. This website also allows registered users to manage genotype and marker/allele frequency files. Registration is optional.

Proper citation: ANCESTRY (RRID:SCR_009121) Copy   

•   Source: SciCrunch Registry

http://www.stsiweb.org/infrastructure/software_data/snp_expectation_maximization_snpem/

Software application for EM algorithm estimations of SNP haplotypes (entry from Genetic Analysis Software)

Proper citation: SNPEM (RRID:SCR_009086) Copy   

•   Source: SciCrunch Registry

http://hasstedt.genetics.utah.edu/

Software application that can (1) compute the likelihood of specified parameter values; (2) compute the probability of each genotype for pedigree members; (3) simulate phenotypes for output into files; (4) maximize the likelihood over specified parameters (with or without standard errors); (5) compute the standard errors of parameters for unknown estimates; (6) simulate phenotypes and estimate parameter values; (7) estimate expected lod score; (8) compute a grid of likelihood over one or two parameters. New additions to V5: assortative mating; TDT; additive multi-locus models (entry from Genetic Analysis Software)

Proper citation: PAP (RRID:SCR_009083) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/qin/FESTA/

Software application (entry from Genetic Analysis Software)

Proper citation: FESTA (RRID:SCR_009081) Copy   

•   Source: SciCrunch Registry

http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.

Proper citation: EHPLUS (RRID:SCR_009159) Copy   

•   Source: SciCrunch Registry

http://www.gene.ucl.ac.uk/public-files/packages/jattwood/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for detecting and displaying well-characterized meiotic breakpoints in human family data.

Proper citation: CROSSFIND (RRID:SCR_009157) Copy   

•   Source: SciCrunch Registry

http://compgen.rutgers.edu/crimappvm.shtml

Software application that is a parallel version of CRIMAP (entry from Genetic Analysis Software)

Proper citation: CRIMAP-PVM (RRID:SCR_009156) Copy   

•   Source: SciCrunch Registry

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

A simulation program that simulates and plots (in real time) ancestral recombination graphs. This is currently primarily a teaching/educational tool. (entry from Genetic Analysis Software)

Proper citation: CHROMOSEG (RRID:SCR_009152) Copy   

•   Source: SciCrunch Registry

http://coding.plantpath.ksu.edu/~jcn/MatLink.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A MATLAB utility for estimating genetic linkage in exotic line-cross mating designs.

Proper citation: MATLINK (RRID:SCR_009148) Copy   

•   Source: SciCrunch Registry

http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application to detect genetically abnormal subjects in a case-control sample based on genotypes at multiple marker loci. (entry from Genetic Analysis Software)

Proper citation: CHECKHET (RRID:SCR_009147) Copy   

•   Source: SciCrunch Registry

http://www.gene.ucl.ac.uk/public-files/packages/linkage_utils/ceph2cri/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application to convert output from CEPH DBMS to CRIMAP format.

Proper citation: CEPH2CRI (RRID:SCR_009143) Copy   

•   Source: SciCrunch Registry

http://www.stat.uchicago.edu/~mcpeek/software/CCQLSpackage1.3/

Software application (entry from Genetic Analysis Software)

Proper citation: CC-QLS (RRID:SCR_009140) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/rarevariant/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2026. Software application for enabling the analysis of rare variants in large-scale case control and quantitative trait association studies. CCRaVAT (Case-Control Rare Variant Analysis Tool) and QuTie (Quantitative Trait) are software packages that enable efficient large-scale analysis of rare variants across specific regions or genome-wide. These programs implement a rare variant super-locus or collapsing method that investigates the accumulation of rare variant alleles in either a case-control or quantitative trait study design. (entry from Genetic Analysis Software)

Proper citation: CCRAVAT (RRID:SCR_009141) Copy   

•   Source: SciCrunch Registry

http://www.stats.ox.ac.uk/~marchini/software.html

A R package for assessing the power of genome-wide association studies using commercially available genotyping chips. The package encapsulates extensive simulation results generated by our program HAPGEN. (entry from Genetic Analysis Software)

Proper citation: GWAPOWER (RRID:SCR_009216) Copy   

•   Source: SciCrunch Registry