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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MENDELSOFT Resource Report Resource Website |
MENDELSOFT (RRID:SCR_013177) | software application, software resource | Software application for identifying all Mendelian inconsistencies in complex pedigree data with thousand of individuals, including many loops and several errors. Can also infer missing genotypes. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, linux/cygwin, ms-windows, macos | is listed by: Genetic Analysis Software | nlx_154474 | SCR_013177 | 2026-08-04 09:43:09 | 0 | ||||||||||
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Mach2dat Resource Report Resource Website 10+ mentions |
Mach2dat (RRID:SCR_009599) | software application, software resource | 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 | 2026-08-04 09:42:25 | 40 | ||||||
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MaCH-Admix Resource Report Resource Website 10+ mentions |
MaCH-Admix (RRID:SCR_009598) | software application, software resource | 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 | 2026-08-04 09:42:24 | 18 | ||||||
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TAGGER Resource Report Resource Website 50+ mentions |
TAGGER (RRID:SCR_009419) | software application, software resource | 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 | 2026-08-04 09:42:22 | 91 | ||||||||||
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SPLINK Resource Report Resource Website 10+ mentions |
SPLINK (RRID:SCR_009414) | software application, software resource | 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 | 2026-08-04 09:42:23 | 46 | ||||||||
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SSAHASNP Resource Report Resource Website 1+ mentions |
SSAHASNP (RRID:SCR_009415) | SSAHASNP | software application, software resource | 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 | 2026-08-04 09:42:22 | 4 | ||||||||
|
SPIP Resource Report Resource Website 100+ mentions |
SPIP (RRID:SCR_009410) | software application, software resource | 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 | 2026-08-04 09:42:22 | 423 | |||||||||
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SPLAT Resource Report Resource Website 10+ mentions |
SPLAT (RRID:SCR_009411) | SPLAT | software application, software resource | 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 | 2026-08-04 09:42:23 | 19 | |||||||
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PLABQTL Resource Report Resource Website 10+ mentions |
PLABQTL (RRID:SCR_012789) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154535 | SCR_012789 | PLAnt Breeding QTL analysis | 2026-08-04 09:43:05 | 14 | |||||||||
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HAPBLOCK 2 Resource Report Resource Website |
HAPBLOCK 2 (RRID:SCR_012788) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, stata | is listed by: Genetic Analysis Software | nlx_154376 | SCR_012788 | 2026-08-04 09:43:05 | 0 | ||||||||||
|
ANNOVAR Resource Report Resource Website 5000+ mentions |
ANNOVAR (RRID:SCR_012821) | ANNOVAR | software application, software resource | 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 | 2026-08-04 09:43:05 | 5946 | |||||
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TOMCAT Resource Report Resource Website 10+ mentions |
TOMCAT (RRID:SCR_013120) | software application, software resource | 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 | 2026-08-04 09:43:08 | 18 | |||||||||
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SASQUANT Resource Report Resource Website 1+ mentions |
SASQUANT (RRID:SCR_013122) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program to estimate genetic effects and heritabilities of quantitative traits in breeding populations consisting of six related generations (entry from Genetic Analysis Software) | gene, genetic, genomic, sas, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154610, biotools:sasquant | https://bio.tools/sasquant | SCR_013122 | 2026-08-04 09:43:08 | 4 | ||||||||
|
SCORE-SEQ Resource Report Resource Website 1+ mentions |
SCORE-SEQ (RRID:SCR_013121) | software application, software resource | 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 | 2026-08-04 09:43:08 | 6 | |||||||||
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QMSIM Resource Report Resource Website 50+ mentions |
QMSIM (RRID:SCR_013123) | software application, software resource | Software application designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154560, biotools:qmsim | https://bio.tools/qmsim | SCR_013123 | Qtl and Marker SIMulator | 2026-08-04 09:43:08 | 57 | ||||||||
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INSEGT Resource Report Resource Website |
INSEGT (RRID:SCR_013126) | software application, software resource | Software application that constructs feasible haplotype configurations and the corresponding segregation types on pedigrees. the haplotype configuration minimizes recombinations on the pedigree. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, (the standard template library, stl, is used) | is listed by: Genetic Analysis Software | nlx_154412 | SCR_013126 | INference of SEGregation Types PANGAEA | 2026-08-04 09:43:08 | 0 | |||||||||
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SPERM Resource Report Resource Website 10+ mentions |
SPERM (RRID:SCR_009409) | software application, software resource | 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 | 2026-08-04 09:42:22 | 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 application, software resource | 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 | 2026-08-04 09:42:26 | 14 | ||||||||
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SNPALYZE Resource Report Resource Website 50+ mentions |
SNPALYZE (RRID:SCR_009401) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows, (98/me/nt4.0/2000/xp) | is listed by: Genetic Analysis Software | nlx_154640 | SCR_009401 | 2026-08-04 09:42:22 | 76 | ||||||||||
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GLFSINGLE/GLFTRIO/GLFMULTIPLES Resource Report Resource Website 1+ mentions |
GLFSINGLE/GLFTRIO/GLFMULTIPLES (RRID:SCR_013128) | software application, software resource | Software application that is a GLF-based variant caller for next-generation sequencing data. It takes one/three/multiple GLF format genotype likelihood files as input and generates a VCF-format set of variant calls as output. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154358 | SCR_013128 | 2026-08-04 09:43:08 | 1 |
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