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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

https://academic.oup.com/bioinformatics/article/21/24/4430/180359

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 7,2025. Software application that is a rank-based meta-analysis method for analyzing results from genome-wide linkage searches. A software package is now available. The gsma software calculates the summed rank for any number of studies and bins, then obtains p-values for the Summed Rank and the Ordered Rank statistics, by simulation. Weighted and unweighted analyses are performed. A test data set is included. (entry from Genetic Analysis Software)

Proper citation: GSMA (RRID:SCR_009214) Copy   

•   Source: SciCrunch Registry

http://ihg.gsf.de/cgi-bin/hw/hwa1.pl (testing part)

Software application that tests for deviation from Hardy-Weinberg equilibrium and tests for association in case controls studies; Plot genotype frequencies graphically using a de Finetti diagram. (entry from Genetic Analysis Software)

Proper citation: FINETTI (RRID:SCR_009179) Copy   

•   Source: SciCrunch Registry

http://www.biostat.harvard.edu/~fbat/fbat.htm

Software application that allows the user to test for association/linkage between disease phenotypes and haplotypes by utilizing family-based controls. The method extends the approach for testing described in Rabinowitz and Laird (2000) to handle multiple tightly linked markers. It is robust to population admixture, yet efficient in the sense that it utilizes data from families where phase cannot be completely resolved in all individuals by using weights, which are estimated from the sample. However, the method remains robust to population stratification and population admixture. The method can handle any type of phenotype, including multiple phenotypes and missing parents, marker data, and/or phase, and provides both bi-allelic and multi-allelic tests. PowerFBAT is a tool for power simulation of association analysis using FBAT with binary outcomes. XWXW is an extension to the Haseman-Elston method for non-parametric linkage test with quantitative traits. XDT is a software that performs classical TDT, SDT and Rabinowitz TDT for nuclear families (not supported anymore). (entry from Genetic Analysis Software)

Proper citation: FBAT (RRID:SCR_009178) Copy   

•   Source: SciCrunch Registry