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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Hapmix Resource Report Resource Website 50+ mentions |
Hapmix (RRID:SCR_004203) | HAPMIX | software application, software resource, source code | Software application that uses genotyping data from SNP arrays for accurately inferring chromosomal segments of distinct continental ancestry in admixed populations, using dense genetic data. (entry from Genetic Analysis Software) | gene, genetic, genomic, admixed, population, genotype, single nucleotide polymorphism, ancestry, chromosomal segment, snp array |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Harvard Medical School; Massachusetts; USA |
NHGRI U01-HG004168; NHLBI R01-HL087699 |
PMID:19543370 | Restricted | nlx_22768, OMICS_02082 | http://www.hsph.harvard.edu/faculty/alkes-price/software/, http://www.stats.ox.ac.uk/~myers/software.html, https://reich.hms.harvard.edu/software | http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004203 | SciCrunch Registry | 2026-10-31 12:20:01 | 52 | ||||
|
Integrated Software Resource Report Resource Website |
Integrated Software (RRID:SCR_004745) | data or information resource, database | A virtual database currently indexing software and tools from the SciCrunch Registry, Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC), Visiome Platform, Cerebellar Platform, Brain Machine Interface Platform, and Genetic Analysis Software (GAS). | database, tool, software, integrated |
is used by: NIF Data Federation is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Visiome Platform is related to: Cerebellar Platform is related to: Brain Machine Interface Platform has parent organization: Integrated |
Data are licensed by their respective owners, Use and distribution is subject to the Terms of Use by the original resource | nlx_75188 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-10 http://neuinfo.org/nif/nifgwt.html?query=nlx_75188, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_75188-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-10 | SCR_004745 | SciCrunch Registry | NIF Integrated Software, NIF Integrated Software View, NIF Software, Integrated Software View | 2026-10-31 12:20:06 | 0 | |||||||
|
ILLUMINUS Resource Report Resource Website |
ILLUMINUS (RRID:SCR_000388) | Illuminus | software application, software resource | A fast and accurate algorithm for assigning single nucleotide polymorphism (SNP) genotypes to microarray data from the Illumina BeadArray technology. | gene, genetic, genomic, c++, single nucleotide polymorphism, genotype, microarray, illumina beadarray, illumina |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:17846035 | Free, Available for download, Freely available | OMICS_00726, nlx_154408 | http://www.sanger.ac.uk/resources/software/illuminus/ | http://www.sanger.ac.uk/science/tools/illuminus | SCR_000388 | SciCrunch Registry | Illuminus: the genotype calling algorithm | 2026-10-31 12:20:54 | 0 | ||||
|
LDB/LDB+ Resource Report Resource Website |
LDB/LDB+ (RRID:SCR_000839) | LDB/LDB+ | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application that integrate genetic linkage map and physical map (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran, unix, sunos | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154413 | SCR_000839 | SciCrunch Registry | Location DataBase | 2026-10-31 12:20:56 | 0 | |||||||
|
HAP 1 Resource Report Resource Website 1+ mentions |
HAP 1 (RRID:SCR_000837) | HAP 1 | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154371 | SCR_000837 | SciCrunch Registry | haplotype resolution using imperfect phylogeny | 2026-10-31 12:20:58 | 3 | |||||||
|
DCHIP LINKAGE Resource Report Resource Website |
DCHIP LINKAGE (RRID:SCR_000835) | DCHIP LINKAGE | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. | gene, genetic, genomic, c++, ms-windows | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154280 | SCR_000835 | SciCrunch Registry | 2026-10-31 12:20:56 | 0 | ||||||||
|
FLOSS Resource Report Resource Website |
FLOSS (RRID:SCR_000836) | FLOSS | software application, software resource | Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (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:floss, nlx_154319 | https://bio.tools/floss | SCR_000836 | SciCrunch Registry | FLexible Ordered SubSet analysis | 2026-10-31 12:20:56 | 0 | |||||||
|
POLYMORPHISM Resource Report Resource Website |
POLYMORPHISM (RRID:SCR_000828) | software application, software resource | Software application for calculating the heterozygosity, PIC, and LIC values for polymorphic markers (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154052 | SCR_000828 | SciCrunch Registry | 2026-10-31 12:20:58 | 0 | |||||||||
|
EDAC Resource Report Resource Website 1+ mentions |
EDAC (RRID:SCR_000829) | EDAC | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154078 | http://www.biostat.wustl.edu/~gc/cgi-bin/calcpwr.cgi | SCR_000829 | SciCrunch Registry | power calculator for Extremely Discordant And Concordant sibpairs | 2026-10-31 12:21:03 | 2 | ||||||
|
2LD Resource Report Resource Website |
2LD (RRID:SCR_000826) | 2LD | software application, software resource | Software program for calculating linkage disequilibrium (LD) measures between two polymorphic markers. | gene, genetic, genomic, c | is listed by: Genetic Analysis Software | PMID:14871868 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154006 | http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software.htm | SCR_000826 | SciCrunch Registry | 2026-10-31 12:20:55 | 0 | ||||||
|
SQTL Resource Report Resource Website |
SQTL (RRID:SCR_000827) | SQTL | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, linux | is listed by: Genetic Analysis Software | Free, Available for download, Freely available | nlx_154032 | SCR_000827 | SciCrunch Registry | Semiparametric QTL mapping in general pedigrees | 2026-10-31 12:20:55 | 0 | |||||||
|
SOLAR Resource Report Resource Website 10+ mentions |
SOLAR (RRID:SCR_000850) | SOLAR | software application, software resource | A flexible and extensive software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of quantitative traits which may involve multiple loci (oligogenic analysis), dominance effects, and epistasis. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran, c, c++, tcl, unix, (solaris 7-10/solaris x86 8-9/digital unix 4.0e/sg irix), linux, macos, ms-windows | is listed by: Genetic Analysis Software | nlx_154653 | http://www.sfbr.org/Departments/genetics_detail.aspx?p=37 | SCR_000850 | SciCrunch Registry | Sequential Oligogenic Linkage Analysis Routines | 2026-10-31 12:21:04 | 23 | |||||||
|
MRH Resource Report Resource Website |
MRH (RRID:SCR_000841) | MRH | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows, unix, solaris | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154493 | SCR_000841 | SciCrunch Registry | Minimum Recombinant Haplotype | 2026-10-31 12:20:58 | 0 | |||||||
|
QTL CAFE Resource Report Resource Website |
QTL CAFE (RRID:SCR_000844) | QTL CAFE | software application, software resource | Software application providing a user freiendly way to perform QTL analysis. The software currently allows 3 types of QTL analysis: (1) single marker ANOVA. (2) marker regression. (3) interval mapping by regression. (entry from Genetic Analysis Software) | gene, genetic, genomic, java | is listed by: Genetic Analysis Software | nlx_154563 | SCR_000844 | SciCrunch Registry | 2026-10-31 12:20:56 | 0 | |||||||||
|
PELICAN Resource Report Resource Website 10+ mentions |
PELICAN (RRID:SCR_001695) | PELICAN | software application, software resource | Software utility for graphically editing the pedigree data files used by programs such as FASTLINK, VITESSE, GENEHUNTER and MERLIN. It can read in and write out pedigree files, saving changes that have been made to the structure of the pedigree. Changes are made to the pedigree via a graphical display interface. The resulting display can be saved as a pedigree file and as a graphical image file. | gene, genetic, genomic, java, pedigree, linkage analysis, editor |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Google Sites |
PMID:15059819 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00215, nlx_154035 | http://www.mrc-bsu.cam.ac.uk/personal/frank/software/pelican/, http://www.rfcgr.mrc.ac.uk/Software/PELICAN/ | SCR_001695 | SciCrunch Registry | Pedigree Editor for LInkage Computer ANalysis | 2026-10-31 12:21:00 | 15 | |||||
|
OSA Resource Report Resource Website 1+ mentions |
OSA (RRID:SCR_002016) | OSA | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software application that allows the researcher to evaluate evidence for linkage even when heterogeneity is present in a data set. This is not an unusual occurrence when studying diseases of complex origin. Families are ranked by covariate values in order to test evidence for linkage among homogeneous subsets of families. Because families are ranked, a priori covariate cutpoints are not necessary. Covariates may include linkage evidence at other genes, environmental exposures, or biological trait values such as cholesterol, age at onset, and so on. | gene, genetic, genomic, c++, unix, solaris, linux |
is listed by: Genetic Analysis Software has parent organization: Duke University; North Carolina; USA |
NIMH R01 MH59528 | PMID:18473393 PMID:15185403 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154504 | http://wwwchg.duhs.duke.edu/software/osa.html | SCR_002016 | SciCrunch Registry | Ordered Subset Analysis, OSA Program, Ordered Subset Analysis Program | 2026-10-31 12:21:00 | 1 | ||||
|
METAL Resource Report Resource Website 1000+ mentions |
METAL (RRID:SCR_002013) | software application, software resource | Software application designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner. (entry from Genetic Analysis Software) | gene, genetic, genomic, whole genome |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:20616382 | nlx_154476, OMICS_00239 | SCR_002013 | SciCrunch Registry | Metal - Meta Analysis Helper, METa AnaLysis Helper | 2026-10-31 12:20:58 | 2413 | ||||||||
|
SVA Resource Report Resource Website 10+ mentions |
SVA (RRID:SCR_002155) | SVA | commercial organization, software application, software resource | Software package to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies. SVA aims to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits. | gene, genetic, genomic, annotate, visualize, genetic variant, next-generation sequencing, whole-genome sequencing, exome, sequencing, genome, disease, trait, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Duke University School of Medicine; North Carolina; USA |
PMID:21624899 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154666, OMICS_00190, biotools:sequencevariantanalyzer | http://www.svaproject.org/, https://bio.tools/sequencevariantanalyzer | SCR_002155 | SciCrunch Registry | Sequence Variant Analyzer, SVA: Sequence Variant Analyzer | 2026-10-31 12:20:59 | 17 | |||||
|
LAMBDAA Resource Report Resource Website |
LAMBDAA (RRID:SCR_001128) | LAMBDAA | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154421 | SCR_001128 | SciCrunch Registry | 2026-10-31 12:20:59 | 0 | ||||||||
|
CAROL Resource Report Resource Website 10+ mentions |
CAROL (RRID:SCR_001800) | CAROL | software application, software resource | Software application that is a combined functional annotation score of non-synonymous coding variants. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, they have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from two bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants. The combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences. (entry from Genetic Analysis Software) The software should run on any UNIX or GNU/Linux system. | gene, genetic, genomic, r, prediction, non-synonymous coding variant |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:22261837 | Free, Available for download, Freely available | nlx_154254, OMICS_00143 | http://www.sanger.ac.uk/resources/software/carol/ | SCR_001800 | SciCrunch Registry | Combined Annotation scoRing toOL | 2026-10-31 12:20:58 | 11 |
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