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http://magest.hgc.jp/

A database for maternal gene expression information for ascidia, colloquially known as sea squirts. Information available includes DNA sequences, expression patterns of ESTs, and cDNA data from uncleaved fertilized eggs. The goal is to utilize the database to understand molecular mechanisms of establishment of embryonic body plans of chordates and to understand evolution from invertebrates to vertebrates in the future.

Proper citation: MAboya Gene Expression Patterns and Sequence Tags (RRID:SCR_000763) Copy   

•   Source: SciCrunch Registry

http://www.homozygositymapper.org/

A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software)

Proper citation: HOMOZYGOSITYMAPPER (RRID:SCR_001714) Copy   

•   Source: SciCrunch Registry

http://eyegene.ophthy.med.umich.edu/madeline/

Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review.

Proper citation: MADELINE (RRID:SCR_001979) Copy   

•   Source: SciCrunch Registry

http://kb.phenoscape.org/

Knowledgebase that uses ontologies to integrate phenotypic data from genetic studies of zebrafish with evolutionary variable phenotypes from the systematic literature of ostariophysan fishes. Users can explore the data by searching for anatomical terms, taxa, or gene names. The expert system enables the broad scale analysis of phenotypic variation across taxa and the co-analysis of these evolutionarily variable features with the phenotypic mutants of model organisms. The Knowledgebase currently contains 565,158 phenotype statements about 2,527 taxa, sourced from 57 publications, as well as 38,189 phenotype statements about 4,727 genes, retrieved from ZFIN. 2013-01-26.

Proper citation: Phenoscape Knowledgebase (RRID:SCR_002821) Copy   

•   Source: SciCrunch Registry

http://www.angis.org.au/Databases/Heart/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The aim of this locus-specific mutation database was to provide an online resource that contains summarized and updated information on familial hypertrophic cardiomyopathy (FHC)-associated mutations and related data, for researchers and clinicians. It also serves as a means of publishing previously unpublished data, which could be of value in understanding genotype/phenotype correlations. This database contains mutations in various genes known to cause familial hypertrophic cardiomyopathy, a genetic disorder associated with defects in the sarcomere [1]. Only gene symbols approved by HUGO are used and mutations are reported in accordance with guidelines recommended by the Mutation Database Initiative of HUGO and EBI.

Proper citation: Familial Hypertrophic Cardiomyopathy DNA Mutation Database (RRID:SCR_002346) Copy   

•   Source: SciCrunch Registry

http://dirline.nlm.nih.gov/

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 15, 2016. Database containing location and descriptive information about a wide variety of information resources including organizations, research resources, projects, and databases concerned with health and biomedicine. This information may not be readily available in bibliographic databases. Each record may contain information on the publications, holdings, and services provided. These information resources fall into many categories including federal, state, and local government agencies; information and referral centers; professional societies; self-help groups and voluntary associations; academic and research institutions and their programs; information systems and research facilities. Topics include HIV/AIDS, maternal and child health, most diseases and conditions including genetic and other rare diseases, health services research and technology assessment. DIRLINE can be searched using subject words (such as disease or condition) including Medical Subject Headings (MeSH) or for the name or location of a resource. It now offers an A to Z list of over 8,500 organizations.

Proper citation: Directory of Health Organizations Online (RRID:SCR_002331) Copy   

•   Source: SciCrunch Registry

http://www.dogmap.ch/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. An international collaboration between 46 labs from 20 different countries towards a low resolution canine marker map under the auspices of the International Society for Animal Genetics (ISAG). The map under development should achieve a resolution of about 20 cM and some of the markers should be mapped physically. The participants have agreed to use microsatellites as markers on a common panel of reference families which will provide the backbone of the marker map. It is foreseen to also include type I markers in the mapping effort and to produce cosmid derived microsatellites for physical mapping. For this purpose part of the effort focuses on the standardization of the canine karyotype. Special attention is payed to hereditary diseases where efforts are under way to establish resource families either by collecting families or by specific breeding. A point of emphasis of the DogMap project is the setting up of an internationally accessible database for handling the mapping data. The structure of the DogMap collaboration includes a managing committee and scientific advisers. The managing committee is responsible for the overall coordination of the activities within the collaboration, for the dissemination of relevant information to all of the participants and for the representation of DogMap outside the collaboration., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DogMap (RRID:SCR_002332) Copy   

•   Source: SciCrunch Registry

http://analysis2.bio-x.cn/myAnalysis.php

A powerful web-based platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci.

Proper citation: SHEsis: Analysis Tools For Random Samples (RRID:SCR_002958) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/#!Synapse:syn4921369/wiki/235539

Portal of PsychENCODE Consortium to study role of rare genetic variants involved in several psychiatric disorders. Database of regulatory elements, epigenetic modifications, RNA and protein in brain.

Proper citation: PsychENCODE Knowledge Portal (RRID:SCR_017500) Copy   

•   Source: SciCrunch Registry

http://www.jurgott.org/linkage/LinkagePC.html

Software application - part of the LINKAGE auxiliary programs (entry from Genetic Analysis Software)

Proper citation: MAKEPED (RRID:SCR_009162) 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 that manage genetic data (entry from Genetic Analysis Software)

Proper citation: DOLINK (RRID:SCR_009163) Copy   

•   Source: SciCrunch Registry

http://kumasakanatsuhiko.jp/projects/disentangler/

Software application that is a visualization technique for linkage disequilibrium mapping and haplotype analysis of multiple multi-allelic genetic markers. (entry from Genetic Analysis Software)

Proper citation: DISENTANGLER (RRID:SCR_009161) Copy   

•   Source: SciCrunch Registry

http://gmc.mdc-berlin.de/alohomora/

Software application designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array. (entry from Genetic Analysis Software)

Proper citation: ALOHOMORA (RRID:SCR_009117) Copy   

•   Source: SciCrunch Registry

http://www.hgu.mrc.ac.uk/Softdata/ALP/

Microsoft Windows application designed to analyze microsatellite DNA fragments separated on an Automated Laser Fluorescence sequencer. (entry from Genetic Analysis Software)

Proper citation: ALP (RRID:SCR_009118) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A tool designed to help visualize the joint effect of genes and continuous environmental covariates on complex human disease simulation models.

Proper citation: SIMULAPLOT (RRID:SCR_009079) Copy   

•   Source: SciCrunch Registry

http://www.stat.uchicago.edu/~wen/tuna/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 22, 2016. Free software package for estimating allele frequencies for all the SNPs available in a population reference panel (e.g. HapMap data base) based on genotype data from a subset of markers (e.g. the Illumina HumanHap300 BeadChip SNP set) in a group of subjects (e.g. the cases in a case-control sample)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TUNA (RRID:SCR_009112) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/caspar.html

Software application who''s main novel feature is conditional linkage analyses, in which the population can be subdivided according to criteria at some loci and analyzed for linkage at other loci. CASPAR uses simulation to overcome the problems inherent in such multiple testing. (entry from Genetic Analysis Software)

Proper citation: CASPAR (RRID:SCR_009074) Copy   

•   Source: SciCrunch Registry

http://www.genenetwork.org/webqtl/main.py

An interactive web site useful for exploring the genetic modulation of thousands of phenotypes gathered over a 30-year period by hundreds of investigators using reference panels of recombinant inbred strains of mice. WebQTL includes dense error-checked genetic maps, as well as extensive gene expression data sets (Affymetrix) acquired across more than 35 strains of mice. WebQTL accepts user-entered traits for BXD, AXB/BXA, CXB, BXH, AKXD recombinant inbred strains. (entry from Genetic Analysis Software)

Proper citation: WEBQTL (RRID:SCR_009072) Copy   

•   Source: SciCrunch Registry

http://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-imprinting/index.html#c63682

Resource no longer in service. Documented on February 23,2021.Software tool as modification of GENEHUNTER software package . Allows for parametric multi-marker linkage analysis of dichotomous traits caused by imprinted genes. By specification of two heterozygote penetrance parameters, paternal and maternal origin of the disease allele can be treated differently in terms of probability of expression of the trait.

Proper citation: genehunter-imprinting (RRID:SCR_009104) Copy   

•   Source: SciCrunch Registry

https://www.helmholtz-muenchen.de/ige/service/software-download/genehunter-modscore/index.html

Software application that is an extension of GENEHUNTER-IMPRINTING, based on the original GENEHUNTER version 2.1 release 6, that allows for a MOD-score analysis, in which parametric LOD scores are maximized over the parameters of the trait model, i.e., the penetrances and disease allele frequency. As of version 2.0, it is possible to use sex-specific recombination frequencies. The genetic positions of markers can be automatically read from a publicly available genetic map. (entry from Genetic Analysis Software)

Proper citation: GENEHUNTER-MODSCORE (RRID:SCR_009069) Copy   

•   Source: SciCrunch Registry