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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SIMLINK Resource Report Resource Website 1+ mentions |
SIMLINK (RRID:SCR_009387) | software resource, software application | Software program to estimate the probability (power) of detecting linkage given family history information on a set of identified pedigrees. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran, ms-dos, unix, sunos, vms | is listed by: Genetic Analysis Software | nlx_154625 | SCR_009387 | 2026-08-01 12:10:50 | 3 | ||||||||||
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SIMLA Resource Report Resource Website 1+ mentions |
SIMLA (RRID:SCR_009385) | software resource, software application | SIMulation program that generates data sets of families for use in Linkage and Association studies. It allows the user flexibility in specifying marker and disease placement, locus heterogeneity, disequilibrium between markers and between markers and disease loci. Output is in the form of a LINKAGE pedigree file and is easily utilized, either directly or with minimal reformatting, as input for various genetic analysis packages (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, solaris, linux | is listed by: Genetic Analysis Software | nlx_154623 | http://wwwchg.duhs.duke.edu/software/simla.html | SCR_009385 | SIMulation of pedigree data for Linkage and Association studies | 2026-08-01 12:11:00 | 1 | ||||||||
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SILCLOD Resource Report Resource Website |
SILCLOD (RRID:SCR_009383) | software resource, software application | Software application to calculate nominal significance levels and critical LOD scores depending on the length of the investigated region, number of chromosomes, and the cross-over rate. The global significance level as well as the precision of the calculation have to be specified. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154619 | http://www.imbs.uni-luebeck.de/pub/silcLOD/index.html | SCR_009383 | SIgnificance Levels and Critical LODs | 2026-08-01 12:10:58 | 0 | ||||||||
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SIBERROR Resource Report Resource Website |
SIBERROR (RRID:SCR_009380) | software resource, software application | Software application that identifies pedigree errors in sibship data. Examples include half siblings, unrelated individuals, identical twins, and parental exclusions. The test statistic is based on the summation of the number of alleles shared by a pair of relatives for a large number of markers and the number of alleles and allele frequencies for those markers. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | nlx_154615 | SCR_009380 | SibError | 2026-08-01 12:11:00 | 0 | |||||||||
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Mach2dat Resource Report Resource Website 10+ mentions |
Mach2dat (RRID:SCR_009599) | software resource, software application | Software that performs logistic regression, using imputed SNP dosage data and adjusting for covariates. | genetic association, genomic analysis, imaging genomics, snp, gene, imputation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MACH 1.0 has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 |
Free, Non-commercial, Acknowledgement requested | nlx_155801 | http://www.nitrc.org/projects/mach2dat | SCR_009599 | Mach2dat: Association with MACH output | 2026-08-01 12:10:52 | 40 | ||||||
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MaCH-Admix Resource Report Resource Website 10+ mentions |
MaCH-Admix (RRID:SCR_009598) | software resource, software application | A genotype imputation software that is an extension to MaCH for faster and more flexible imputaiton, especially in admixed populations. It has incorporated a novel piecewise reference selection method to create reference panels tailored for target individual(s). This reference selection method generates better imputation quality in shorter running time. MaCH-Admix also separates model parameter estimation from imputation. The separation allows users to perform imputation with standard reference panels + pre-calibrated parameters in a data independent fashion. Alternatively, if one works with study-specific reference panels, or isolated target population, one has the option to simultaneously estimate these model parameters while performing imputation. MaCH-Admix has included many other useful options and supports VCF input files. All existing MaCH documentation applies to MaCH-Admix. | genomic analysis, imaging genomics, imputation, snp, gene, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:23074066 | Free, Non-commercial, Acknowledgement requested | nlx_155800, biotools:mach-admix | http://www.nitrc.org/projects/mach-admix, https://bio.tools/mach-admix | SCR_009598 | MaCH-Admix: Genotype Imputation Software | 2026-08-01 12:11:00 | 18 | ||||||
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TAGGER Resource Report Resource Website 50+ mentions |
TAGGER (RRID:SCR_009419) | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, web-based |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154669 | SCR_009419 | 2026-08-01 12:10:59 | 91 | ||||||||||
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SPLINK Resource Report Resource Website 10+ mentions |
SPLINK (RRID:SCR_009414) | software resource, software application | Software application for linkage analysis using affected sib pairs (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, sunos, ms-dos | is listed by: Genetic Analysis Software | nlx_154659 | http://www-gene.cimr.cam.ac.uk/clayton/software/ | SCR_009414 | affected Sib Pairs LINKage analysis | 2026-08-01 12:11:01 | 46 | ||||||||
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SSAHASNP Resource Report Resource Website 1+ mentions |
SSAHASNP (RRID:SCR_009415) | SSAHASNP | software resource, software application | 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) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154661 | SCR_009415 | Sequence Search and Alignment by Hashing Algorithm for SNP detection | 2026-08-01 12:10:50 | 4 | ||||||||
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SPIP Resource Report Resource Website 100+ mentions |
SPIP (RRID:SCR_009410) | software resource, software application | Software application that simulate pedigrees and genetic data in age-structured populations (entry from Genetic Analysis Software) | gene, genetic, genomic, c | is listed by: Genetic Analysis Software | nlx_154657 | SCR_009410 | Simulate Pedigree In Population | 2026-08-01 12:10:50 | 423 | |||||||||
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SPLAT Resource Report Resource Website 10+ mentions |
SPLAT (RRID:SCR_009411) | SPLAT | software resource, software application | 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. | gene, genetic, genomic, c++, qt, unix, sunos, linux, macos, ms-windows, (2000/xp) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154658 | SCR_009411 | Sib Pair Linkage Analysis Testing | 2026-08-01 12:11:01 | 19 | |||||||
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PLABQTL Resource Report Resource Website 10+ mentions |
PLABQTL (RRID:SCR_012789) | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154535 | SCR_012789 | PLAnt Breeding QTL analysis | 2026-08-01 12:11:01 | 14 | |||||||||
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HAPBLOCK 2 Resource Report Resource Website |
HAPBLOCK 2 (RRID:SCR_012788) | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, stata | is listed by: Genetic Analysis Software | nlx_154376 | SCR_012788 | 2026-08-01 12:11:02 | 0 | ||||||||||
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ANNOVAR Resource Report Resource Website 5000+ mentions |
ANNOVAR (RRID:SCR_012821) | ANNOVAR | software resource, software application | 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) | genomic analysis, imaging genomics, next generation sequencing, snp, gene, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: wANNOVAR has parent organization: OpenBioinformatics.org |
PMID:20601685 | Free | nlx_154225, biotools:annovar, OMICS_00165 | https://bio.tools/annovar, https://bio.tools/annovar | SCR_012821 | functional ANNOtation of genetic VARiants, ANNOVAR: Functional annotation of genetic variants | 2026-08-01 12:11:02 | 5946 | |||||
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LifeGene Resource Report Resource Website 10+ mentions |
LifeGene (RRID:SCR_010524) | LifeGene | biomaterial supply resource, material resource | 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. | environment, disease, gene, lifestyle, health, child, adult, longitudinal, genetic test, survey |
is listed by: One Mind Biospecimen Bank Listing is related to: University of Gothenburg; Gothenburg; Sweden is related to: Karolinska Institute; Stockholm; Sweden is related to: Lund University; Lund; Sweden is related to: Umea University; Umea; Sweden is related to: Uppsala University; Uppsala; Sweden is related to: Linkoping University; Linkoping; Sweden has parent organization: Karolinska Institute; Stockholm; Sweden |
General population, Volunteer | Swedish Research Council ; Karolinska Institutet; Stockholm; Sweden ; AFA Foundation ; Torsten Foundation ; Ragnar Soderberg Foundation |
With approval, Must have Swedish Institute connections | nlx_20757 | http://lifegene.ki.se/working_groups/sampling_en.html | SCR_010524 | 2026-08-01 12:11:02 | 29 | |||||
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TOMCAT Resource Report Resource Website 10+ mentions |
TOMCAT (RRID:SCR_013120) | software resource, software application | 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) | gene, genetic, genomic, java, 5.0 | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154681 | SCR_013120 | 2026-08-01 12:10:53 | 18 | |||||||||
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SCORE-SEQ Resource Report Resource Website 1+ mentions |
SCORE-SEQ (RRID:SCR_013121) | software resource, software application | 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) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154611 | SCR_013121 | SCORE-type tests for detecting disease associations with rare variants in SEQuencing Studies | 2026-08-01 12:11:01 | 6 | |||||||||
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SPERM Resource Report Resource Website 10+ mentions |
SPERM (RRID:SCR_009409) | software resource, software application | 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. | gene, genetic, genomic, fortran77 | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154656 | SCR_009409 | 2026-08-01 12:10:59 | 16 | |||||||||
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Solar Eclipse Imaging Genetics tools Resource Report Resource Website 10+ mentions |
Solar Eclipse Imaging Genetics tools (RRID:SCR_009645) | Solar Eclipse Imaging Genetics tools | software resource, software application | 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 | c++, genetic association, genomic analysis, gifti, imaging genomics, linux, loni pipeline, macos, microsoft, nifti, posix/unix-like, snp, gene, windows, windows xp, genetics, neuroimaging, heritability, pleiotropy, quantitative trait loci, genome-wide association, gene expression, methylation, trait, structural neuroimaging, functionalneuroimaging, brain imaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Non-commercial, Open Software License, v3, Http://www.nitrc.org/include/glossary.php#552 | nlx_155966 | SCR_009645 | 2026-08-01 12:10:52 | 14 | ||||||||
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Movement Disorders Biobank Resource Report Resource Website |
Movement Disorders Biobank (RRID:SCR_010659) | MDBB | biomaterial supply resource, material resource | 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. | dna, fibroblast, movement disorder, neurodegeneration, brain iron accumulation disorder, dystonia, parkinson's disease, phenotype, genotype, gene, biobank |
is listed by: One Mind Biospecimen Bank Listing is related to: EuroBioBank has parent organization: EuroBioBank |
Movement disorder, Neurodegeneration with Brain Iron Accumulation disorder, Dystonia, Parkinson's disease | nlx_69108 | http://www.istituto-besta.it/Area-Ricerca.aspx?doc=Elenco-Unita-Operative&IdUO=UO-NEUROGENETICAMOLECOLARE | SCR_010659 | 2026-08-01 12:10:52 | 0 |
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