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http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Bio++ (RRID:SCR_016055) Copy
http://bioinformatics.ust.hk/BOOST.html
Software application (entry from Genetic Analysis Software) for a method for detecting gene-gene interactions. It allows examining all pairwise interactions in genome-wide case-control studies.
Proper citation: BOOST (RRID:SCR_013133) Copy
i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System. The i2b2 Center is developing a scalable informatics framework that will enable clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origin. For some resources (e.g. software) the use of the resource requires accepting a specific (e.g. OpenSource) license.
Proper citation: Informatics for Integrating Biology and the Bedside (RRID:SCR_013629) Copy
http://www.nitrc.org/projects/nusdast
A repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia, healthy controls and their respective siblings, most with 2-year longitudinal follow-up. The data include neuroimaging data, cognitive data, clinical data, and genetic data.
Proper citation: Northwestern University Schizophrenia Data and Software Tool (NUSDAST) (RRID:SCR_014153) Copy
https://ihg.helmholtz-muenchen.de/cgi-bin/hw/hwa1.pl
Software tool for performing tests for deviation from Hardy-Weinberg equilibrium and tests for association. Used in population-based genetic association studies to identify susceptibility genes for complex diseases.
Proper citation: Tests for deviation from Hardy-Weinberg equilibrium (RRID:SCR_016496) Copy
Platform for analysis of the genetics of cardiovascular disease.Used for searching and analysis of human genetic information linked to myocardial infarction, atrial fibrillation and related traits while protecting the integrity and confidentiality of the data.
Proper citation: Cardiovascular Disease Knowledge Portal (RRID:SCR_016536) Copy
https://www.ncbi.nlm.nih.gov/projects/mutagene/
Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity.
Proper citation: MutaGene (RRID:SCR_016574) Copy
https://github.com/BDI-pathogens/phyloscanner
Software tool for analysing pathogen genetic diversity and relationships between and within hosts at once, in windows along genome. Inferring transmission from within and between host pathogen genetic diversity.
Proper citation: phyloscanner (RRID:SCR_017400) Copy
https://beast.community/tempest
Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019.
Proper citation: TempEst (RRID:SCR_017304) Copy
Open access database of all types of genetic variation data from all species. Users can download data from any study, or submit their own data to archive. You can also query all variants by study, gene, chromosomal location or dbSNP identifier using our Variant Browser.
Proper citation: European Variation Archive (EVA) (RRID:SCR_017425) Copy
https://github.com/ctlab/GADMA
Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data.
Proper citation: GADMA (RRID:SCR_017680) Copy
http://geneatlas.roslin.ed.ac.uk
Database of associations between traits and variants using UK Biobank cohort. Searchable atlas of genetic associations. Assists researchers to query UK Biobank. Provides unbiased view of phenotype and genotype associations across of traits.
Proper citation: GeneATLAS (RRID:SCR_017577) Copy
A long-term health research project which follows pregnant women and their offspring in a continuous health and developmental study. More than 14,000 mothers enrolled during pregnancy in 1991 and 1992, and the health and development of their children has been followed in great detail. The ALSPAC families have provided a vast amount of genetic and environmental information over the years which can be made available to researchers globally.
Proper citation: ALSPAC (RRID:SCR_007260) Copy
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
Center for investigators studying human health and disease, offering the opportunity to assess the causes of disease, and new treatment methods in nonhuman primate models that closely recapitulate humans. Its mission is to provide interdisciplinary programs in biomedical research on significant human health-related problems in which nonhuman primates are the models of choice.
Proper citation: California National Primate Research Center (RRID:SCR_006426) Copy
https://www.broadinstitute.org/ccle/
A collaborative project between the Broad Institute and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation, with the goal of conducting a detailed genetic and pharmacologic characterization of a large panel of human cancer models. The CCLE also works to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.
Proper citation: Cancer Cell Line Encyclopedia (RRID:SCR_013836) Copy
https://cran.r-project.org/web/packages/ibdreg/index.html
Software package in S-PLUS and R to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree. (entry from Genetic Analysis Software)
Proper citation: IBDREG (RRID:SCR_013127) Copy
https://www.ars-grin.gov/npgs/
Cooperative effort by U.S. state and federal government and private organizations to preserve the genetic diversity of plants. The NPGS aids scientists and the need for genetic diversity by acquiring, preserving, evaluating, documenting and distributing crop germplasm. The NPGS is managed by the Agricultural Research Service (ARS), the in-house research agency of the United States Department of Agriculture (USDA). Funding for the NPGS comes primarily through appropriations from the U.S. Congress.
Proper citation: National Plant Germplasm System (NPGS) (RRID:SCR_016785) Copy
https://bitbucket.org/nicofmay/basta-bayesian-structured-coalescent-approximation/src/master/
Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations.
Proper citation: BASTA (RRID:SCR_017303) Copy
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
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