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http://www.fged.org/

Society that develop standards for biological research data quality, annotation and exchange. They facilitate the creation and use of software tools that build on these standards and allow researchers to annotate and share their data easily. They promote scientific discovery that is driven by genome wide and other biological research data integration and meta-analysis. Historically, FGED began with a focus on microarrays and gene expression data. However, the scope of FGED now includes data generated using any technology when applied to genome-scale studies of gene expression, binding, modification and other related applications.

Proper citation: FGED (RRID:SCR_001897) 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://bnmc.caltech.edu/

The Beckman Institute BNMC brings together researchers from many disciplines at Caltech to address problems in the mechanistic modeling of coupled genomic, intercellular and intracellular processes. It represents an attempt to encourage closer interaction and collaboration between groups in Biology, Control and Dynamical Systems, and the Center for Advanced Computing Research. The focus of BNMC is biochemical phenomena occurring within and between cells, in particular the mechanistic modeling of molecular networks of all kinds (e.g., transcriptional, regulatory, metabolic, signal transduction, mechanical, etc.) with and without spatial variation and intercellular communication. BNMC is formed as a coordinated effort aimed at (1) applying existing capabilities to collaboratively solve biological modeling problems that arise in answering scientific questions in Caltech laboratories, (2) exploring a diversity of novel approaches in order to achieve fundamental advances necessary to address the classes of modeling problems biologists want to solve, and (3) organizing projects to better share human experience as well as common infrastructure to avoid duplication and maximize solution interoperability.

Proper citation: Caltech, The Beckman Institute: The Biological Network Modeling Center (RRID:SCR_008060) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/blocks.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application aiming at identifying haplotype blocks. The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low. (entry from Genetic Analysis Software)

Proper citation: ENTROPY BLOCKER (RRID:SCR_000123) 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://weatherby.genetics.utah.edu/cgi-bin/Phevor/PhevorWeb.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Tool that integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. It works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant prioritization tools. It does so using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single exome and family trio-based diagnostic analyses, the most commonly occurring clinical scenarios, and ones for which existing personal-genomes diagnostic tools are most inaccurate and underpowered. Phevor not only improves diagnostic accuracy for individuals presenting with established disease phenotypes, but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases, or known disease-causing alleles.

Proper citation: Phevor (RRID:SCR_002273) 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://www.acgtinc.com

Company which provides a suite of molecular biology and genomic services, including DNA sequencing by Sanger and Next Generation Sequencing. All services are offered at a research, GLP or clinical grade levels.

Proper citation: ACGT Inc. (RRID:SCR_001026) Copy   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

Proper citation: FASTLINK (RRID:SCR_009177) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 7, 2016.

Proper citation: FASTEHPLUS (RRID:SCR_009176) 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 for non-parametric analysis (entry from Genetic Analysis Software)

Proper citation: ERPA (RRID:SCR_009173) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/ExomePicks

Software application that suggests individuals to be sequenced in a large pedigree. ExomePicks assumes that a genotyping chip or another cost effective means will be used to determine IBD sharing in the pedigree and that, subsequently, one would like to sequence a minimal number of individuals and use their sequences together with IBD information to deduce the sequence of other individuals in the pedigree. We are currently using it in the context of whole exome and whole genome sequencing studies to pick individuals to be sequenced from large family collections. (entry from Genetic Analysis Software)

Proper citation: EXOMEPICKS (RRID:SCR_009174) Copy   

•   Source: SciCrunch Registry

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

Software application to calculate pair-wise linkage disequilibrium based on SNP genotype data from unrelated individuals. EM algorithm is used to estimate pair-wise haplotype frequencies. The output file is in the format of input file for GOLD program, thus it can be directly plug into GOLD to get LD plots. (entry from Genetic Analysis Software)

Proper citation: EMLD (RRID:SCR_009171) Copy   

•   Source: SciCrunch Registry

http://www.ibms.sinica.edu.tw/~csjfann/first%20flow/programlist.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that for detecting linkage/disequilibrium signals # between genetic markers and disease loci, particularly if only one # or a few large pedigrees are available. The strategy differs from # conventional approaches that require at least a moderate number of # families to attain adequate statistical power. The proposed testing # procedure is advantageous in that it provides high statistical power # coupled with reduced sample collection. Furthermore, the proposed # method avoids problems such as potential population stratification # and genetic heterogeneity, and is robust with respect to misspecification # of phenotype. (entry from Genetic Analysis Software)

Proper citation: EPDT (RRID:SCR_009172) Copy   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

Proper citation: EH (RRID:SCR_009168) Copy   

•   Source: SciCrunch Registry

http://www.columbia.edu/~ws2267/SOFT/EAGLET/eaglet.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software package that provides a number of improved statistics for detecting linkage and estimating trait location. EAGLET uses multiple subsamples of dense SNP data to detect linkage with increased power, and to construct sharp 95% confidence intervals for the true trait location.

Proper citation: EAGLET (RRID:SCR_009166) Copy   

•   Source: SciCrunch Registry

http://nephrologie.uniklinikum-leipzig.de/nephrologie.site,postext,easylinkage.html

Software application that combines automated setup and performance of linkage analyses and simulation. The program package supports currently single-point linkage analyses, multi-point linkage analyses, and the simulation package SLink, and provides genome-wide as well as chromosomal postscript plots of LOD scores, NPL scores, P values, and other parameters. The software can analyze STRPs as well as SNP chip data from Affymetrix, Illumina, or self-defined SNP data. The program performs single- and multi-point simulation studies.

Proper citation: EASYLINKAGE/EASYLINKAGE-PLUS (RRID:SCR_009167) Copy   

•   Source: SciCrunch Registry

http://wwwcsif.cs.ucdavis.edu/~gusfield/dpph.html

Software application that is similar to the BPPH program (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DPPH (RRID:SCR_009164) Copy   

•   Source: SciCrunch Registry

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

Software program that allows students and scientists to explore potential manifestations of genetic models and stochastic processes. It also provides a means to evaluate the effectiveness of statistical procedures such as linkage analysis or QTL detection. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GREGOR (RRID:SCR_009165) Copy   

•   Source: SciCrunch Registry