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http://wpicr.wpic.pitt.edu/WPICCompGen/newcovibd/covibd.htm

Software application that refines linkage analysis of affected sibpairs by considering attributes or environmental exposures thought to affect disease liability. This refinement utilizes a mixture model in which a disease mutation segregates in only a fraction of the sibships, with the rest of the sibships unlinked. Covariate information is used to predict membership within the two groups corresponding to the linked and unlinked sibships. The pre-clustering model uses covariate information to first form two probabilistic clusters and then tests for excess IBD-sharing in the clusters. The Cov-IBD model determines probabilistic group membership by joint consideration of covariate and IBD values. (entry from Genetic Analysis Software)

Proper citation: COVIBD (RRID:SCR_009155) Copy   

•   Source: SciCrunch Registry

https://neuinfo.org/mynif/search.php?list=cover&q=*

Service that partners with the community to expose and simultaneously drill down into individual databases and data sets and return relevant content. This type of content, part of the so called hidden Web, is typically not indexed by existing web search engines. Every record links back to the originating site. In order for NIF to directly query these independently maintained databases and datasets, database providers must register their database or dataset with the NIF Data Federation and specify permissions. Databases are concept mapped for ease of sharing and to allow better understanding of the results. Learn more about registering your resource, http://neuinfo.org/nif_components/disco/interoperation.shtm Search results are displayed under the Data Federation tab and are categorized by data type and nervous system level. In this way, users can easily step through the content of multiple resources, all from the same interface. Each federated resource individually displays their query results with links back to the relevant datasets within the host resource. This allows users to take advantage of additional views on the data and tools that are available through the host database. The NIF site provides tutorials for each resource, indicated by the Professor Icon professor icon showing users how to navigate the results page once directed there through the NIF. Additionally, query results may be exported as an Excel document. Note: NIF is not responsible for the availability or content of these external sites, nor does NIF endorse, warrant or guarantee the products, services or information described or offered at these external sites. Integrated Databases: Theses virtual databases created by NIF and other partners combine related data indexed from multiple databases and combine them into one view for easier browsing. * Integrated Animal View * Integrated Brain Gene Expression View * Integrated Disease View * Integrated Nervous System Connectivity View * Integrated Podcasts View * Integrated Software View * Integrated Video View * Integrated Jobs * Integrated Blogs For a listing of the Federated Databases see, http://neuinfo.org/mynif/databaseList.php or refer to the Resources Listed by NIF Data Federation table below.

Proper citation: NIF Data Federation (RRID:SCR_004834) Copy   

•   Source: SciCrunch Registry

http://galton.uchicago.edu/~junzhang/LAPSTRUCT.html

Software application to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1) geometrically motivated and graphic model based; (2)robustness of outliers. (entry from Genetic Analysis Software)

Proper citation: LAPSTRUCT (RRID:SCR_007550) Copy   

•   Source: SciCrunch Registry

http://www.pedigree-draw.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software)

Proper citation: Pedigree-Draw (RRID:SCR_008302) Copy   

•   Source: SciCrunch Registry

http://www.people.fas.harvard.edu/~junliu/em/em.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program.

Proper citation: EM-DECODER (RRID:SCR_000023) Copy   

•   Source: SciCrunch Registry

http://lpg.nci.nih.gov/lpg_small/protocols/HapScope/

Software application that includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. (entry from Genetic Analysis Software)

Proper citation: HAPSCOPE (RRID:SCR_000838) Copy   

•   Source: SciCrunch Registry

http://mlemire.freeshell.org/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software application with implementation of the Sad statistic, more robust to transmission ratio distortion in the context of allele sharing (entry from Genetic Analysis Software)

Proper citation: GENEHUNTER SAD (RRID:SCR_000831) Copy   

•   Source: SciCrunch Registry

http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/comds

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2022. Software application for combined segregation and linkage analysis, incorporating severity and diathesis. (entry from Genetic Analysis Software)

Proper citation: COMDS (RRID:SCR_000832) Copy   

•   Source: SciCrunch Registry

http://www.genetics.emory.edu/labs/epstein/software/chaplin/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Software application for identifying specific haplotypes or haplotype features that are associated with disease using genotype data from a case-control study. (entry from Genetic Analysis Software)

Proper citation: CHAPLIN (RRID:SCR_000833) Copy   

•   Source: SciCrunch Registry

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

Software application for constructing multilocus linkage map (entry from Genetic Analysis Software)

Proper citation: CRIMAP (RRID:SCR_000834) Copy   

•   Source: SciCrunch Registry

Issue

https://cran.r-project.org/web/packages/adegenet/index.html

Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)

Proper citation: ADEGENET (RRID:SCR_000825) Copy   

•   Source: SciCrunch Registry

http://research.i2r.a-star.edu.sg:8080/kleisli/demos/pedigree/

Software application (entry from Genetic Analysis Software)

Proper citation: PEDIGREE-VISUALIZER (RRID:SCR_000842) Copy   

•   Source: SciCrunch Registry

http://vorlon.case.edu/~jxl175/haplotyping.html

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. Software application for inferring haplotypes from genotypes on pedigree data (entry from Genetic Analysis Software)

Proper citation: PEDPHASE (RRID:SCR_000843) Copy   

•   Source: SciCrunch Registry

http://animalgene.umn.edu/locusmap/index.html

Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software)

Proper citation: LOCUSMAP (RRID:SCR_000840) Copy   

•   Source: SciCrunch Registry

http://www-genome.wi.mit.edu/ftp/pub/software/rhmapper/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. An interactive software program for radiation hybrid mapping (entry from Genetic Analysis Software)

Proper citation: RHMAPPER (RRID:SCR_000845) Copy   

•   Source: SciCrunch Registry

http://gusevlab.org/projects/germline/

Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GERMLINE (RRID:SCR_001720) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/olorin

An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software)

Proper citation: OLORIN (RRID:SCR_002015) Copy   

•   Source: SciCrunch Registry

https://sites.pitt.edu/~weeks/docs/SimIBD.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)

Proper citation: SIMIBD (RRID:SCR_002094) Copy   

•   Source: SciCrunch Registry

http://gmt.genome.wustl.edu/packages/breakdancer/

A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software)

Proper citation: BREAKDANCER (RRID:SCR_001799) Copy   

•   Source: SciCrunch Registry

http://haplopainter.sourceforge.net/

A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software)

Proper citation: HAPLOPAINTER (RRID:SCR_001710) Copy   

•   Source: SciCrunch Registry