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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ZOOM Resource Report Resource Website 100+ mentions |
ZOOM (RRID:SCR_002175) | ZOOM | commercial organization, software resource | Software to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity. | next-generation sequencing, illumina, solexa, reference genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:18684737 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01852, biotools:zoom | https://bio.tools/zoom | SCR_002175 | ZOOM: Next Gen Sequencing | 2026-08-04 09:40:35 | 278 | |||||
|
TWOLOC Resource Report Resource Website |
TWOLOC (RRID:SCR_009230) | TWOLOC | software application, software resource | Software package for analyzing two-locus susceptibility gene models in affected sib-pair data (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran77, pascal, awk, unix, (saloris/dec unix/irix/..), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154387, biotools:twoloc | https://bio.tools/twoloc | SCR_009230 | 2026-08-04 09:42:20 | 0 | ||||||||
|
GENERECON Resource Report Resource Website 1+ mentions |
GENERECON (RRID:SCR_009195) | GENERECON | software application, software resource | Software application for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, linux, macos, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154338, biotools:generecon | https://bio.tools/generecon | SCR_009195 | 2026-08-04 09:42:19 | 1 | ||||||||
|
HTR Resource Report Resource Website 1+ mentions |
HTR (RRID:SCR_009241) | HTR | software application, software resource | Software application for haplotype association mapping using unrelated individuals; fixed and sliding window analysis; overall tests and tests for individual haplotype effects (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, bash shell, ms-windows, unix, solaris, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154402, biotools:htr | https://bio.tools/htr | SCR_009241 | Haplotype Trend Regression | 2026-08-04 09:42:20 | 1 | |||||||
|
MULTIDISEQ Resource Report Resource Website |
MULTIDISEQ (RRID:SCR_009304) | MULTIDISEQ | software application, software resource | A multipoint linkage analysis software which allows Marker-Marker LD (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154494, biotools:multidiseq | https://bio.tools/multidiseq | SCR_009304 | 2026-08-04 09:42:20 | 0 | ||||||||
|
MPDA Resource Report Resource Website 10+ mentions |
MPDA (RRID:SCR_009303) | MPDA | software application, software resource | A tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. MPDA was developed under the software platform, MATLABR, and provided user-friendly interfaces adapted to Windows systems (Windows 98, Windows 2000 and Windows XP). or users without installing software MATLABR, we also developed stand-alone executables generated via the MATLABR compiler. MPDA provides four major functions: (1) Whole-genome DNA amplification/hybridization analysis, (2) Allele frequency estimation, (3) Association mapping, (4) Allelic imbalance detection. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data. (entry from Genetic Analysis Software) | gene, genetic, genomic, matlabr, ms-windows, (windows98/2000/xp), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:mpda, nlx_154492 | https://bio.tools/mpda | SCR_009303 | Microarray Pooled DNA Analyser | 2026-08-04 09:42:21 | 12 | |||||||
|
SWEEP Resource Report Resource Website 10+ mentions |
SWEEP (RRID:SCR_009418) | SWEEP | software application, software resource | Software application that allows large-scale analysis of haplotype structure in genomes for the primary purpose of detecting evidence of natural selection. Primarily, it uses the Long Range Haplotype test to look for alleles of high frequency with long-range linkage disequilibrium, which suggest the haplotype rapidly rose to high frequency before recombination could break down associations with nearby markers. SWEEP takes phased genotype data as input, detects all haplotype blocks in that data, and then determines the frequency and long-range LD for each allele in each block. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:sweep, nlx_154667 | https://bio.tools/sweep | SCR_009418 | 2026-08-04 09:42:22 | 32 | ||||||||
|
SUMSTAT Resource Report Resource Website 10+ mentions |
SUMSTAT (RRID:SCR_009416) | software application, software resource | Software application that assess the joint disease association of multiple unlinked SNPs via sums of SNP specific test statistics. Genome-wide significance levels are obtained by per mutation analysis. (entry from Genetic Analysis Software) | gene, genetic, genomic, free pascal, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154663, biotools:sumstat | https://bio.tools/sumstat | SCR_009416 | 2026-08-04 09:42:22 | 11 | |||||||||
|
SUP Resource Report Resource Website |
SUP (RRID:SCR_009417) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,6th, 2021. Software application as extension to SLINK/FastSLINK to allow more marker loci to be simulated in pedigrees conditional on trait values and in linkage equilibrium or disequilibrium with trait locus. entry from Genetic Analysis Software. | gene, genetic, genomic, c, c++, unix, linux, cygwin, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is related to: SLINK is related to: FASTSLINK is related to: bio.tools |
PMID:16803631 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154664, biotools:sup | https://bio.tools/sup | SCR_009417 | Slink Utility Program | 2026-08-04 09:42:23 | 0 | ||||||
|
SASGENE Resource Report Resource Website |
SASGENE (RRID:SCR_013084) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program for gene segregation and linkage analysis in breeding population (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 | biotools:sasgene, nlx_154608 | https://bio.tools/sasgene | SCR_013084 | 2026-08-04 09:43:08 | 0 | ||||||||
|
SNPTEST Resource Report Resource Website 100+ mentions |
SNPTEST (RRID:SCR_009406) | software application, software resource | Software program for the analysis of single SNP association in genome-wide studies. The tests implemented can cater for binary (case-control) and quantitative phenotypes, can condition upon an arbitrary set of covariates and properly account for the uncertainty in genotypes. The program is designed to work seamlessly with the output of both the genotype calling program CHIAMO, the genotype imputation program IMPUTE and the program GTOOL. This program was used in the analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC). (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154651, biotools:snptest | https://bio.tools/snptest | http://www.stats.ox.ac.uk/~marchini/software/gwas/snptest.html | SCR_009406 | 2026-08-04 09:42:22 | 396 | ||||||||
|
TASSEL Resource Report Resource Website 1000+ mentions |
TASSEL (RRID:SCR_012837) | TASSEL | software application, software resource | Software package which performs a variety of genetic analyses including association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information. These new analyses should permit association analysis in a wide range plant and animal species. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, web-based, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
nlx_154674, biotools:tassel | http://sourceforge.net/projects/tassel/, https://bio.tools/tassel | SCR_012837 | and Linkage, Trait Analysis by aSSociation, Evolution | 2026-08-04 09:43:05 | 2335 | |||||||
|
ECLIPSE Resource Report Resource Website 100+ mentions |
ECLIPSE (RRID:SCR_013130) | software application, software resource | A set of three programs, preproc, eclipse2 and eclipse3 which analyze genetic marker data for genotypic errors and pedigree errors. Using a single preprocessing program (preproc), eclipse2 analyzes data on pairs of individuals, and eclise3 analyzes data jointly on trios. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, tested on, unix, (compaq tru64 v5.0a), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154290, biotools:eclipse | https://bio.tools/eclipse | SCR_013130 | Error Correcting Likelihoods In Pedigree Structure Estimation. PANGAEA | 2026-08-04 09:43:08 | 121 | ||||||||
|
SKAT Resource Report Resource Website 100+ mentions |
SKAT (RRID:SCR_009396) | software application, software resource | Software application that is a SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes. SKAT aggregates individual score test statistics of SNPs in a SNP set and efficiently computes SNP-set level p-values, e.g. a gene or a region level p-value, while adjusting for covariates, such as principal components to account for population stratification. SKAT also allows for power/sample size calculations for designing for sequence association studies. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154634, biotools:skat | https://bio.tools/skat | SCR_009396 | SNP-set (Sequence) Kernel Association Test | 2026-08-04 09:42:22 | 273 | ||||||||
|
SIMPED Resource Report Resource Website 1+ mentions |
SIMPED (RRID:SCR_009388) | software application, software resource | Software program that quickly generates haplotypes and/or genotype data for a large number of marker loci (>20,000) for pedigrees of virtually any size and complexity. Haplotypes and/or genotypes are generated using user specified genetic map distances and haplotypes and/or allele frequencies. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, ms-window, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:simped, nlx_154627 | https://bio.tools/simped | http://www.hgsc.bcm.tmc.edu/genemapping | SCR_009388 | 2026-08-04 09:42:22 | 1 | ||||||||
|
SIBLINK Resource Report Resource Website |
SIBLINK (RRID:SCR_009381) | software application, software resource | Software application that allows the user to perform multipoint linkage analysis based on estimated IBD sharing between affected sibpairs. IBD sharing is inferred from IBS status, given marker genotypes, frequencies, and locations. Resulting LOD scores are maximized across a grid of possible disease locations and IBD sharing vectors. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, solaris, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:siblink, nlx_154616 | https://bio.tools/siblink | http://wwwchg.duhs.duke.edu/software/siblink.html | SCR_009381 | 2026-08-04 09:42:22 | 0 | ||||||||
|
THESIAS Resource Report Resource Website 50+ mentions |
THESIAS (RRID:SCR_013449) | THESIAS | software application, software resource | Software program that performs haplotype-based association analysis in unrelated individuals. This program is based on a maximum likelihood model described in Tregouet et al. 2002 and is linked to the stochastic EM (SEM) algorithm. THESIAS allows the simultaneous estimation of haplotype frequencies and of their associated effects on the phenotype of interest. In its current version, both quantitative and qualitative phenotypes can be studied. Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can be investigated. (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btm058 | nlx_154102, OMICS_19747, biotools:tHESIAS | https://bio.tools/THESIAS, https://sources.debian.org/src/thesias/ | http://ecgene.net/genecanvas/downloads.php?cat_id=1 | SCR_013449 | Testing Haplotype EffectS In Association Studies | 2026-08-04 09:43:13 | 51 | |||||
|
QmRLFS-finder Resource Report Resource Website 10+ mentions |
QmRLFS-finder (RRID:SCR_014584) | software application, software resource, data analytics software | A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis. | r-loop, r loop, rlf, rlfs, dna, rna, input sequences, output files, annotation, analysis, bio.tools |
uses: UCSC Genome Browser is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
Singapore Agency for Science Technology and Research | PMID:26400173 PMID:25883153 |
Open Source | biotools:qmrlfs-finder | https://omictools.com/qmrlfs-finder-tool, https://bio.tools/qmrlfs-finder | SCR_014584 | QmRLFS finder | 2026-08-04 09:43:28 | 13 | |||||
|
FunRich: Functional Enrichment analysis tool Resource Report Resource Website 100+ mentions |
FunRich: Functional Enrichment analysis tool (RRID:SCR_014467) | software application, standalone software, software resource, data analytics software | A software tool used for functional enrichment and interaction network analysis of genes and proteins. Users can search against a default background database or load customized database. The results can be depicted as venn, bar, column, pie and doughnut charts. | network analysis, background database, charts, data analytics software, standalone software, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
PMID:25921073 PMID:26149235 |
Public, Open Source | biotools:funrich | https://bio.tools/funrich | SCR_014467 | 2026-08-04 09:43:27 | 338 | |||||||
|
SNP HITLINK Resource Report Resource Website |
SNP HITLINK (RRID:SCR_013340) | SNP HITLINK | software application, software resource | Software program providing a useful pipeline to directly connect SNP data and linkage analysis program. SNP HiTLink currently supports the data from SNP chips provided by Affymetrix (Mapping 100k/500k array set, Genome-Wide Human SNP array 5.0/6.0) and Illumina (recently supported), carrying out typical linkage analysis programs of MLINK (FASTLINK/ LINKAGE package), Superlink, Merlin and Allegro. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154644, biotools:snp_hitlink | https://bio.tools/snp_hitlink | SCR_013340 | SNP HIgh-Throughput LINKage analysis system | 2026-08-04 09:43:11 | 0 |
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