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http://www.sanger.ac.uk/science/tools/ssahasnp-0

A polymorphism detection tool that detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. For those less repetitive or non-repetitive reads, we place them uniquely on the reference genome sequence and find the best alignment according to the pair-wise alignment score if there are multiple seeded regions. From the best alignment, SNP candidates are screened, taking into account the quality value of the bases with variation as well as the quality values in the neighbouring bases, using neighbourhood quality standard (NQS). For insertions/deletions, we check if the same indel is mapped by more than one read, ensuring the detected indel with high confidence. (entry from Genetic Analysis Software)

Proper citation: SSAHASNP (RRID:SCR_009415) Copy   

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http://www.loni.usc.edu/Software/moreinfo.php?package=BGE

A JAVA application designed to create taxonomies or hierarchies in order to classify and organize information.

Proper citation: BrainGraph Editor (RRID:SCR_009536) Copy   

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https://swfsc.noaa.gov/textblock.aspx?Division=FED&id=3434

Software application that simulate pedigrees and genetic data in age-structured populations (entry from Genetic Analysis Software)

Proper citation: SPIP (RRID:SCR_009410) Copy   

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http://www.joslinresearch.org/LabSites/Krolewski/splat/

Software application that can calculate virtually any linkage test statistic under several sib pair study designs: affected, discordant, unaffected, and pairs defined by threshold values for quantitative traits, such as extreme discordant sib pairs. It uses the EM algorithm to compute maximum likelihood estimates of sharing (subject to any user-specified domain restrictions or null hypotheses) and then plots lod scores versus chromosomal position. It includes a novel grid scanning capability that enables simultaneous visualization of multiple test statistics. Phenotype definitions can be modified without recalculating inheritance vectors, thereby providing considerable analytical flexibility. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPLAT (RRID:SCR_009411) Copy   

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https://plant-breeding.uni-hohenheim.de/software.html#jfmulticontent_c110647-2

Software application (entry from Genetic Analysis Software)

Proper citation: PLABQTL (RRID:SCR_012789) Copy   

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http://www.bonebank.com

Biotechnology company dedicated to enhancing quality of patient care through development and manufacture of safe, high quality allograft solutions for healthcare professionals.

Proper citation: Texas Human Biologics (RRID:SCR_010523) Copy   

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http://econpapers.repec.org/software/bocbocode/s438902.htm

Software application (entry from Genetic Analysis Software)

Proper citation: HAPBLOCK 2 (RRID:SCR_012788) Copy   

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http://www.openbioinformatics.org/annovar/

An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software)

Proper citation: ANNOVAR (RRID:SCR_012821) Copy   

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https://www.lifegene.se/In-english/

Swedish study to get a better understanding of how genes, environment and way of life affect health that will enable access to the longitudinal data on 500,000 participants after ethical approval. Half a million people in Sweden between the ages of 0 and 45 will be recruited as volunteers for 6 to 8 years. People between 18 and 45 will be invited and they may, in turn, bring children and other people that they live with into the project. Participants will be followed for many years with regular online surveys and health checks. Their blood and urine samples will also be stored in a biobank. All the data will form a very large information base, where researchers can follow what happens with people''''s health. The LifeGene test center will measure height, hip, waist and chest measurements. A so-called spirometry test will be conducted which measures lung function, a hearing test and bioimpedance measurement (includes weight, BMI and distribution of body fat and muscle mass). They also take blood and urine samples and measure blood pressure and pulse. LifeGene foresees a lot of different research cooperation. Everything from simple withdrawal of longitudinal data, leverage of LifeGene infrastructure and cooperation between LifeGene and complementing scientific projects covering specific areas in more depth. LifeGene will enable access to unique longitudinal data on 500,000 participants available for researchers after ethical approval. LifeGene is also an infrastructure with Test Centers covering most of Sweden, logistics for sample management from arm-to-freezer and state-of-the-art large scale automatic biobanking enabling low cost, high quality, fast withdrawal of biological samples.

Proper citation: LifeGene (RRID:SCR_010524) Copy   

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http://www.psbc.org/home/index.htm

At Puget Sound Blood Center, when we talk about the work of our Research Institute, what we are really talking about is saving lives. Many recognize the lifesaving work of the Blood Center for its role in maintaining the blood supply for Western Washington. But that is only the beginning of how the Blood Center touches the lives of people all over the world. The Blood Center is widely considered the premier knowledge source on blood research and transfusion medicine and has been developing cutting-edge technologies and establishing best practices in this field for over sixty-six years. Medical institutions worldwide rely on the Blood Center''s research work. Scientific equipment manufacturers, as well as pharmaceutical companies turn to the Blood Center for help in developing effective equipment and successful therapies that are saving lives around the world every day.

Proper citation: Puget Sound Blood Center (RRID:SCR_010527) Copy   

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https://www.dkfz.de/en/epidemiologie-krebserkrankungen/software/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May24,2023. Software program that implements the Mantel statistics as proposed by Beckmann et al. (2005) to test for association between genetic markers and phenotypes in case-control studies using haplotype information. The potential value of haplotypes has attracted widespread interest in the mapping of complex traits. Haplotype sharing methods take into account linkage disequilibrium information between multiple markers, and may have good power to detect predisposing genes. We present a new approach based on Mantel statistics for space time clustering, which we developed in order to improve the power of haplotype sharing analysis for gene mapping in complex disease. The new statistic correlates genetic similarity and phenotypic similarity across pairs of haplotypes for case-only and case-control studies. The genetic similarity is measured as the shared length between haplotypes around a putative disease locus. Alternative measures for the phenotypic similarity were implemented. (entry from Genetic Analysis Software)

Proper citation: TOMCAT (RRID:SCR_013120) Copy   

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http://dlin.web.unc.edu/software/SCORE-Seq/

A command-line program for detecting disease associations with rare variants in sequencing studies. The mutation information is aggregated across multiple variant sites of a gene through a weighted linear combination and then related to disease phenotypes through appropriate regression models. The weights can be constant or dependent on allele frequencies and phenotypes. The association testing is based on score-type statistics. The allele-frequency threshold can be fixed or variable. Statistical significance can be assessed by using asymptotic normal approximation or resampling. The current release covers binary and continuous traits with arbitrary covariates under case-control and cross-sectional sampling. (entry from Genetic Analysis Software)

Proper citation: SCORE-SEQ (RRID:SCR_013121) Copy   

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https://www.genetics.ucla.edu/software/download?package=4

Software application for analysis of sperm typing data. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPERM (RRID:SCR_009409) Copy   

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http://www.ohsu.edu/xd/education/schools/school-of-medicine/departments/clinical-departments/pathology/research/oregon-brain-bank.cfm

Brain bank that harvests, banks and disperses postmortem tissue for use in brain and medical research. It also provides neuropathologic diagnoses of organic dementia in a cohort of NIH sponsored research subjects. The bank includes tissue primarily from patients with Alzheimer's but also includes Huntington's, Parkinson's, and other disorders.

Proper citation: Oregon Brain Bank (RRID:SCR_013085) Copy   

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http://www.nitrc.org/projects/se_linux/

Software tools optimized for performing univariate and multivariate imaging genetics analyses while providing practical correction strategies for multiple testing. The goal of this project is to merge two important research directions in modern science, genetics and neuroimaging. This entails combining modern statistical genetic methods and quantitative phenotyping performed with high dimensional neuroimaging modalities. So far, however, standard imaging tools are unable to deal with large-scale genetics data, and standard genetics tools, in turn, are unable to accommodate large size and binary format of the image data. Their focus is to create imaging genetics tools for classical genetic and epigenetic epidemiological analyses such as heritability, pleiotropy, quantitative trait loci (QTL) and genome-wide association (GWAS), gene expression, and methylation analyses optimized for traits derived from structural and functional brain imaging data

Proper citation: Solar Eclipse Imaging Genetics tools (RRID:SCR_009645) Copy   

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http://www.jcm.riken.go.jp/

The Microbe Division in RIKEN-BRC has been collecting, preserving, and distributing cultured microbial strains as one of the leading culture collections in the world since established as Japan Collection of Microorganisms (JCM) in 1981. JCM aims to contribute to scientific communities by maintaining and serving high-quality microbial resources useful for general microbial studies and various research fields particularly in health and environmental science. JCM has participated in the National BioResource Project supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan as the core facility for General Microbes. JCM maintains approximately 19,900 strains as of Sept. 2010, and the approximate numbers of the available strains from JCM are: 7,400 strains of aerobic and anaerobic bacteria including actinomycetes, 300 strains of archaea, and 4,100 strains of fungi including yeasts (in total ca. 12,000 strains). Strains held at JCM are limited to those classified in Risk Group 1 or 2. Information of the available strains is opened to the public through the JCM On-line Catalogue Database. Genomic DNA samples of some strains are also distributed in cooperation with RIKEN BRC-DNA Bank. More than 3,500 strains are annually distributed to domestic and overseas researchers. JCM welcomes a deposit of microbial strains published or designed to be published in scientific papers as well as an order for microbial cultures.

Proper citation: JCM (RRID:SCR_010653) Copy   

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http://perlprimer.sourceforge.net/

A free, open-source GUI software application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing.

Proper citation: PerlPrimer (RRID:SCR_012038) Copy   

•   Source: SciCrunch Registry

http://www.psoriasis.org/netcommunity/act_biobank

The National Psoriasis Victor Henschel BioBank is a collection of biological samples and clinical information used by qualified scientists to further the field of psoriasis genetics. Once completed, the National Psoriasis BioBank will be the largest collection of psoriasis DNA samples in the world, moving us closer to understanding the causes of psoriatic diseases, discovering more and better treatments and finding a cure. The BioBank is currently collecting DNA from people with and without psoriasis and/or psoriatic arthritis. Simply by donating your DNA����??a blood sample and a swab of your cheek cells����??and providing us with your medical history, you can help us find a cure. Samples will be processed and stored at a private laboratory and not at the National Psoriasis Foundation. The National Psoriasis BioBank is part of the Genetic Alliance BioBank (GA BioBank), a centralized repository for the collection, storage and distribution of biological samples (including DNA, serum, cells and tissues) and clinical data for genetic researchers.

Proper citation: National Psoriasis BioBank (RRID:SCR_010537) Copy   

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http://www.eurobiobank.org/en/partners/description/inncb_copy.htm#organisation

A biobank of human biological material and genetic information. It provides samples and information to researchers in order to identify new genes and clarify pathogenic mechanisms of diseases. The biobank offers biochemical and molecular diagnoses of genetic dystonias, Parkinson's disease and NBIA disorders, as well as storage of biological samples for external institutions.

Proper citation: Movement Disorders Biobank (RRID:SCR_010659) Copy   

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http://www.sph.umich.edu/csg/yli/whait/

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

Proper citation: WHAIT (RRID:SCR_009425) Copy   

•   Source: SciCrunch Registry