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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ALTree Resource Report Resource Website 1+ mentions |
ALTree (RRID:SCR_007562) | data processing software, software application, software resource, data analysis software | Software package to perform phylogeny based association and localization analysis.Used for association detection and localization of susceptibility sites using haplotype phylogenetic trees. Performs these two phylogeny-based analysis: tests association between candidate gene and disease; pinpoints markers (SNPs) that are putative disease susceptibility loci. | phylogeny based association, association detection, susceptibility sites, haplotype phylogenetic trees, gene, genetic, genomic |
is listed by: Genetic Analysis Software is listed by: Debian |
PMID:16595555 DOI:10.1093/bioinformatics/btl131 |
Free, Available for download, Freely available | OMICS_13032, nlx_154221 | https://sources.debian.org/src/altree/, https://gitlab.inria.fr/NGS/ALTree, | SCR_007562 | ALTREE | 2026-08-04 09:41:53 | 3 | ||||||
|
PROGENY Resource Report Resource Website 100+ mentions |
PROGENY (RRID:SCR_006647) | Progeny | software application, commercial organization, software resource, data management software | Fully customizable, comprehensive genetic pedigree and clinical data management software including a multi-user relational database with an integrated pedigree drawing component to manage genetic and pedigree data in one database. Manage Pedigrees, Individuals, SNPs, STRs, Samples, Plates, Genotypes and exports to multiple analysis platforms. (entry from Genetic Analysis Software) * LIMS software, providing advanced sample tracking and management (including functionality to generate and record barcodes) and configurable workflows for your specific environment. * Full genotype management gives users the ability to track not only family-based studies, but Whole Genome Association studies containing 1000''s of samples with large arrays. | gene, genetic, genomic, c++, active x control, ms-windows, pedigree, clinical, genotype, data management, drawing, family history, questionnaire, sample, lab management, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software |
nlx_154553, OMICS_00216 | SCR_006647 | Progeny Software LLC, Progeny Software | 2026-08-04 09:41:39 | 407 | ||||||||
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MAIA Resource Report Resource Website 100+ mentions |
MAIA (RRID:SCR_007153) | MAIA | data processing software, software application, software resource, data analysis software | Software package of programs for complex segregation analysis in animal pedigrees. | gene, genetic, genomic, segregation, analysis, animal, pedigree |
is listed by: Genetic Analysis Software has parent organization: Institute of Cytology and Genetics of the Siberian Branch of the RAS; Novosibirsk; Russia |
Free, Non-commercial, Change of source code requires permission | nlx_154435 | SCR_007153 | 2026-08-04 09:41:47 | 349 | ||||||||
|
SIFT Resource Report Resource Website 10000+ mentions |
SIFT (RRID:SCR_012813) | SIFT | data analysis service, source code, analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available. | gene, genetic, genomic, amino acid, substitution, protein function, coding region, single nucleotide variant, coding indel, deletion, insertion, sequence, protein, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SIFT 4G has parent organization: Genome Institute of Singapore; Singapore; Singapore has parent organization: J. Craig Venter Institute |
Agency for Science Technology and Research ; NIGMS GM29009 |
PMID:19561590 PMID:12824425 PMID:11337480 DOI:10.1038/nprot.2009.86 |
Non-commercial | biotools:sift, OMICS_00137, nlx_154618 | http://sift.jcvi.org/, https://bio.tools/sift, https://sources.debian.org/src/sift/ | http://sift.bii.a-star.edu.sg/SIFT.html | SCR_012813 | Sorting Intolerant From Tolerant | 2026-08-04 09:43:05 | 10223 | |||
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ARP.GEE Resource Report Resource Website 1+ mentions |
ARP.GEE (RRID:SCR_013134) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application that simultaneously estimates a trait-locus position and its genetic effects for affected relative pairs (ARP) by one of two methods. Either allow a different trait-locus effect for each ARP type, or constrain the trait-locus effects according to the marginal effect of a single susceptibility locus. We include a goodness of fit statistic for the constrained model. (entry from Genetic Analysis Software) | gene, genetic, genomic, r/s-plus | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154206, nlx_154232, SCR_009108 | SCR_013134 | R/ARP.GEE | 2026-08-04 09:43:08 | 7 | ||||||||
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PolyPhen: Polymorphism Phenotyping Resource Report Resource Website 1000+ mentions |
PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) | PolyPhen, PolyPhen-2, POLYPHEN | simulation software, data processing software, data analysis software, software resource, software application | Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs. | annotate, nonsynonymous, SNP, predict, coding, damaging, effect, missense, mutation, sequence, variant, phenotype, genetic, disease, exon, protein, coding, fraction, genome, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Harvard University; Cambridge; United States |
PMID:20354512 PMID:23315928 |
SCR_013200, OMICS_00136, nlx_154540, nif-0000-21329, biotools:polyphen, SCR_013238 | https://bio.tools/polyphen | http://www.bork.embl-heidelberg.de/PolyPhen/ | SCR_013189 | PolyPhen, POLYPHEN, PolyPhen-2, Polymorphism Phenotyping, Polymorphism Phenotyping v2 | 2026-08-04 09:43:09 | 4151 | |||||
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ALLELIX Resource Report Resource Website 1+ mentions |
ALLELIX (RRID:SCR_009115) | ALLELIX | data analysis service, analysis service resource, software resource, software application, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 23, 2013. Software application / data analysis service where one can enter the alleles of commonly used STR by clicking the mouse. The algorithm calculates the paternity index and the Essen-Moeller probability of kinship for the deficiency- and the trio case. Everybody can use the network-software online after registering. The usage on the internet is free. Academic users can ask me to unlock an option to display the details (formulas/frequencies etc.) and to have an export-funktion to MS Word. The program is in German and (non-professional) English. An expansion to other languages is easy, if somebody helps us with the translation. For those who are interested to have the software running on their own intranet (for database security reasons) an individual agreement can be found. (entry from Genetic Analysis Software) (German version is: http://www.allelix.de) | gene, genetic, genomic, c++, java script, ms-windows, (2000 &iis/me & personal webserver) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154216 | SCR_009115 | Allelix - Paternity Linkage Analysis Online | 2026-08-04 09:42:18 | 2 | |||||||
|
GENEPOP Resource Report Resource Website 1000+ mentions |
GENEPOP (RRID:SCR_009194) | Genepop | data processing software, software application, software resource, data analysis software | Population genetic data analysis software package. Used to perform exact Hardy Weinberg Equilibrium test. Used for population differentiation and for genotypic disequilibrium among pairs of loci. Computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc. and performs analyses of isolation by distance from pairwise comparisons of individuals or population samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Population, differentation, genetic, data, analysis, Hardy Weinberg Equilibrium test, statistics, genotyping, disequilibrium, pair, loci, allele, frequency |
is listed by: Genetic Analysis Software is listed by: CRAN |
PMID:21585727 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154337 | https://kimura.univ-montp2.fr/~rousset/Genepop.htm, https://cran.r-project.org/web/packages/genepop/index.html | SCR_009194 | genepop'007 | 2026-08-04 09:42:19 | 2266 | |||||
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BARS Resource Report Resource Website 10+ mentions |
BARS (RRID:SCR_009123) | BARS | software application, software resource | Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, linux, 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_154204, biotools:bars, nlx_154228, SCR_009106 | https://bio.tools/bars | SCR_009123 | Bayesian Adaptive Regression Splines | 2026-08-04 09:42:17 | 39 | ||||||
|
CMAP Resource Report Resource Website 100+ mentions |
CMAP (RRID:SCR_009034) | CMap | data processing software, software application, software resource, data analysis software | Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, unix, solaris, freebsd, linux, sequence, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite has parent organization: Generic Model Organism Database Project works with: Drug Gene Budger |
PMID:19648141 | GNU General Public License | nlx_153998, OMICS_00933 | https://sourceforge.net/projects/gmod/files/cmap/ | http://www.gmod.org/cmap/, http://gmod.org/wiki/Cmap | SCR_009034 | , GMOD Comparative Mapping (CMap) tool, Comparative Mapping tool, genetic and comparative maps | 2026-08-04 09:42:17 | 413 | ||||
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Haploview Resource Report Resource Website 5000+ mentions |
Haploview (RRID:SCR_003076) | Haploview | data processing software, software application, software resource, source code | A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site. | linkage disequilibrium, haplotype, genotype, visualization, analysis, single nucleotide polymorphism, gene, genetic, genomic, java |
is listed by: Genetic Analysis Software is listed by: SoftCite is related to: International HapMap Project is related to: PLINK has parent organization: Broad Institute |
PMID:15297300 PMID:21356869 PMID:20147036 |
Free, Available for download, Freely available | nif-0000-30472 | http://www.broad.mit.edu/personal/jcbarret/haploview/ | SCR_003076 | 2026-08-04 09:40:48 | 6933 | ||||||
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QGene Resource Report Resource Website 100+ mentions |
QGene (RRID:SCR_003209) | QGene | simulation software, data processing software, source code, data analysis software, software resource, software application | A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request. | gene, genetic, genomic, java, qtl mapping, trait analysis, trait, population, simulation, map, quantitative trait locus, comparison, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Kansas State University; Kansas; USA |
NSF DBI 0109879; USDA-NRI Applied Plant Genomics Program 2004-35317-14867 |
PMID:18940826 | Free, Available for download, Freely available | biotools:qgene, nif-0000-31383 | https://bio.tools/qgene | http://coding.plantpath.ksu.edu/qgene | SCR_003209 | QGene - Software for QTL data exploration | 2026-08-04 09:40:51 | 126 | |||
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SIMM Resource Report Resource Website 1+ mentions |
SIMM (RRID:SCR_000849) | simulation software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Gene dropping simulation software. The program is a gzip'ed tar archive and is designed to run under UNIX/Linux operating system. | gene, genetic, genomic, software | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154626 | http://mlemire.freeshell.org/software.html | SCR_000849 | SimM | 2026-08-04 09:40:15 | 2 | |||||||
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MACH 1.0 Resource Report Resource Website 50+ mentions |
MACH 1.0 (RRID:SCR_001759) | data processing software, software application, software resource, data analysis software | A Markov Chain based software tool for haplotyping, genotype imputation and disease association analysis that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. | gene, genetic, genomic, haplotype, genotype, genomic analysis, imaging genomics, imputation, snp, gene, haplotyping, sequence |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Mach2dat has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 |
Free | nlx_154202, OMICS_00064 | SCR_001759 | MArkov Chain Haplotyper MINIMAC, MArkov Chain Haplotyping | 2026-08-04 09:40:27 | 58 | |||||||
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SNAP - SNP Annotation and Proxy Search Resource Report Resource Website 100+ mentions |
SNAP - SNP Annotation and Proxy Search (RRID:SCR_002127) | SNAP | data analysis service, analysis service resource, software resource, software application, production service resource, service resource | A computer program and web-based service for the rapid retrieval of linkage disequilibrium proxy single nucleotide polymorphism (SNP) results given input of one or more query SNPs and based on empirical observations from the International HapMap Project and the 1000 Genomes Project. A series of filters allow users to optionally retrieve results that are limited to specific combinations of genotyping platforms, above specified pairwise r2 thresholds, or up to a maximum distance between query and proxy SNPs. SNAP can also generate linkage disequilibrium plots | gene, genetic, genomic, r, oracle, single nucleotide polymorphism, linkage disequilibrium, genotypeing array, physical distance, membership, proxy, plot |
is listed by: OMICtools is listed by: Genetic Analysis Software is related to: International HapMap Project is related to: 1000 Genomes: A Deep Catalog of Human Genetic Variation has parent organization: Broad Institute |
NHLBI N01-HC-65226 | PMID:18974171 | Free, Freely Available | OMICS_01927, nlx_154638 | http://www.broad.mit.edu/mpg/snap/ | SCR_002127 | SNAP (SNP Annotation and Proxy Search), SNAP 2, SNP Annotation and Proxy Search | 2026-08-04 09:40:34 | 144 | ||||
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GATK Resource Report Resource Website 10000+ mentions |
GATK (RRID:SCR_001876) | GATK | data processing software, data analysis software, software resource, software application, software library, software toolkit | A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software) | gene, genetic, genomic, next-generation resequencing, bio.tools |
is used by: Halvade Somatic is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SnpEff is related to: GATK HaplotypeCaller is related to: GATK VariantFiltration has parent organization: Broad Institute |
PMID:21478889 | Free, Available for download, Freely available | nlx_154324, OMICS_00286, biotools:gatk | http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit, https://bio.tools/gatk | SCR_001876 | Genome Analysis ToolKit | 2026-08-04 09:40:29 | 16663 | |||||
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VAAST Resource Report Resource Website 10+ mentions |
VAAST (RRID:SCR_002179) | VAAST, VAAST 2 | data processing software, data analysis software, standalone software, software resource, sequence analysis software, software application | A probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST combines elements of phylogenetic conservation, amino acid substitution, and aggregative approaches to variant prioritization into a single unified likelihood-framework that allows users to accurately identify damaged genes and deleterious variants. The software can score both coding (SNV, indel and splice site) and non-coding variants (SNV), evaluating the cumulative impact of both types of variants simultaneously. It can identify rare variants causing rare genetic diseases and can also use both rare and common variants to identify genes responsible for common diseases. | sequence analysis software, genetic, variant classifier, amino acid substitution, disease, genome interpretation, variant prioritization, disease gene prioritization, genomic variation, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: Opal Research has parent organization: Yandell Lab Portal |
PMID:23836555 PMID:21700766 |
Free, Freely available | nlx_154686, SciRes_000138, biotools:vaast, OMICS_02134 | https://bio.tools/vaast | SCR_002179 | Variant Annotation Analysis and Search Tool, Variant Annotation Analysis & Search Tool | 2026-08-04 09:40:35 | 30 | |||||
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SOAP Resource Report Resource Website 100+ mentions |
SOAP (RRID:SCR_000689) | SOAP, | data processing software, software application, software resource | Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, next generation sequencing, alignment, short read, bio.tools |
lists: SOAPfusion lists: SOAPfuse lists: SOAPnuke lists: GapCloser is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: BGI; Shenzhen; China is parent organization of: SOAP3 is parent organization of: SOAPaligner/soap2 |
PMID:18227114 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154652, biotools:soap | https://bio.tools/soap | SCR_000689 | SOAP: short oligonucleotide alignment program, Short Oligonucleotide Analysis Package | 2026-08-04 09:40:12 | 402 | |||||
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LDHEATMAP Resource Report Resource Website 100+ mentions |
LDHEATMAP (RRID:SCR_006312) | software application, software resource | Software application that plots measures of pairwise linkage disequilibria for SNPs (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154424, SCR_009347, nlx_154561 | http://stat-db.stat.sfu.ca:8080/statgen/research/LDheatmap | SCR_006312 | R/LDHEATMAP | 2026-08-04 09:41:33 | 160 | ||||||||
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HCLUST Resource Report Resource Website 1000+ mentions |
HCLUST (RRID:SCR_009154) | HCLUST | software application, software resource | Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, 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:h-clust, SCR_009102, nlx_154195, nlx_154331 | https://bio.tools/h-clust | SCR_009154 | R/HCLUST | 2026-08-04 09:42:18 | 1459 |
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