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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RELATIVEFINDER Resource Report Resource Website 1+ mentions |
RELATIVEFINDER (RRID:SCR_009356) | RELATIVEFINDER | software resource, software application | Software program for checking relationships between pairs of individuals. There are many excellent programs that carry out similar tasks. Some of the unique features in relativeFinder are the batch mode options, that allow large jobs to be divided into many smaller jobs (suitable for deployment on a compute cluster environment), and the flexibility of the underlying Merlin engine, which allows relative finder to handle large pedigrees and consider a variety of alternate relationships -- including potential relationships specified by the user on the fly. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154571 | SCR_009356 | 2026-02-13 10:56:23 | 2 | |||||||||
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REAPER Resource Report Resource Website 10+ mentions |
REAPER (RRID:SCR_009354) | REAPER | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Tag SNP selection tool according to r2-bins method that is specifically designed for full genome scale deterministic tagging. | gene, genetic, genomic, windows, linux |
is listed by: Genetic Analysis Software has parent organization: University of Tartu; Tartu; Estonia |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154569 | SCR_009354 | 2026-02-13 10:56:23 | 11 | ||||||||
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QU-GENE Resource Report Resource Website 1+ mentions |
QU-GENE (RRID:SCR_009351) | QU-GENE | software resource, software application | Software package for quantitative analysis of genetic models (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran, ms-windows | is listed by: Genetic Analysis Software | nlx_154566 | SCR_009351 | QUantitative GENEtics | 2026-02-13 10:56:23 | 6 | ||||||||
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RISCALW Resource Report Resource Website |
RISCALW (RRID:SCR_009352) | RISCALW | software resource, software application | Windows program for risk calculation in families with Duchenne muscular dystrophy. It is based on an extended genetic model which includes germline mosaicism and different new mutation rates depending on sex and mutation type. Arbitrary family structures and additional diagnostic information like genotypes from intragenetic and flancing genetic markers of the dystrophin gene, creatin kinase values and female deletion test results can be taken into account. (entry from Genetic Analysis Software) | gene, genetic, genomic, delphi 4, ms-windows | is listed by: Genetic Analysis Software | Duchenne muscular dystrophy | nlx_154567 | SCR_009352 | RISk CALculation in Windows | 2026-02-13 10:56:23 | 0 | |||||||
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PSEUDOMARKER.M Resource Report Resource Website 1+ mentions |
PSEUDOMARKER.M (RRID:SCR_009346) | PSEUDOMARKER.M | software resource, software application | A set of programs written in MATLAB for the analysis of QTL data from inbred line crosses. (entry from Genetic Analysis Software) | gene, genetic, genomic, matlab | is listed by: Genetic Analysis Software | nlx_154558 | SCR_009346 | 2026-02-13 10:56:23 | 1 | |||||||||
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PSEUDO Resource Report Resource Website 1+ mentions |
PSEUDO (RRID:SCR_009344) | PSEUDO | software resource, software application | Software application that estimates genomewide empirical p-values for Kong and Cox tests of linkage using the replicate pool method, which for many data sets, improves upon the computational efficiency of conventional gene-dropping methods by several orders of magnitude. This allows Pseudo to handle data sets with large families and makes it particularly applicable to those situations where p-value estimation by standard methods is computationally prohibitive. Pseudo also estimates variance for reported p-values, produces graphical and text summaries of results, and is able to assess significance of multiple correlated outcomes. Pseudo is designed to work with the Merlin package and includes utilities for generating input files from standard Merlin output. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, c++, linux, unix, macos, ms-windows |
is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:16832873 | nlx_154556 | SCR_009344 | 2026-02-13 10:56:23 | 4 | ||||||||
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SAS/GENETICS Resource Report Resource Website 100+ mentions |
SAS/GENETICS (RRID:SCR_009343) | SAS/GENETICS | software resource, software application | Software application for summarizing marker properties (allele & genotype frequencies, tests for Hardy-Weinberg equilibrium, measures of marker informativeness), examining marker-marker relationships (tests and measures of linkage disequilibrium, and haplotype frequency estimation), and exploring marker-trait associations using case-control or family-based tests (entry from Genetic Analysis Software) | gene, genetic, genomic, c, ms-windows, unix, (hpux/aixr/solaris/..), mvs | is listed by: Genetic Analysis Software | nlx_154609 | SCR_009343 | 2026-02-13 10:56:23 | 120 | |||||||||
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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 | 2026-02-13 10:56:24 | 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 | 2026-02-13 10:56:24 | 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 | 2026-02-13 10:56:24 | 4 | ||||||||
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SEQUENCE LD/SEQUENCE LDHOT Resource Report Resource Website |
SEQUENCE LD/SEQUENCE LDHOT (RRID:SCR_009379) | software resource, software application | Software program that analyzes sequence data. It obtains an approximation to the likelihood of a summary of the data (as such it can be thought of as a marginal likelihood approach). It does not use all the information in the data, but computationally it can be substantially more efficient than the full-likelihood methods (and hence able to analyze larger data sets). (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154614 | http://www.maths.lancs.ac.uk/~fearnhea/Software.html | SCR_009379 | 2026-02-13 10:56:23 | 0 | |||||||||
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SDMINP Resource Report Resource Website |
SDMINP (RRID:SCR_009377) | SDMINP | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software program for fast calculation of empirical and adjusted p-values for correlated and uncorrelated hypotheses in multiple testing experiments. It is based on the Free Step-Down Resampling Method for controlling the Family Wise Error Rate, originally proposed by Westfall and Young (1993), and implements a variation of the efficient algorithm of Ge et al. (2003), in which the originally necessary re-sampling effort was reduced considerably and the method made computationally more feasible. The program is independent of the underlying test statistic and works with provided observed and permutation test statistics. (entry from Genetic Analysis Software) | gene, genetic, genomic, python 2.3.5, unix, linux, ms-windows | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154612 | http://www.dkfz.de/SDMinP/ | SCR_009377 | Step-Down MIN P-value | 2026-02-13 10:56:23 | 0 | ||||||
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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 | 2026-02-13 10:56:24 | 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 | 2026-02-13 10:56:24 | 19 | |||||||
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R/SNP.PLOTTER Resource Report Resource Website 1+ mentions |
R/SNP.PLOTTER (RRID:SCR_009376) | software resource, software application | An R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either Portable Document Format (PDF) or Encapsulated (EPS) files. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154599, SCR_009405, nlx_154649 | https://github.com/cannin/snp_plotter | http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html | SCR_009376 | SNP.PLOTTER | 2026-02-13 10:56:23 | 2 | |||||||
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R/METASIM Resource Report Resource Website 1+ mentions |
R/METASIM (RRID:SCR_009370) | software resource, software application | An R package that uses an individual-based approach to simulate distributions of genotypes that result from arbitrary within and among population demographies (including extinction/recolonization). These distributions can be used to test new or existing population-genetics summary statistics or develop null distributions under various demographies. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, c++, unix, ms-windows, macos | is listed by: Genetic Analysis Software | nlx_154592 | http://linum.cofc.edu/software.html | SCR_009370 | METApopulation SIMulation | 2026-02-13 10:56:23 | 1 | ||||||||
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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 | 2026-02-13 10:56:24 | 16 | |||||||||
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SNPALYZE Resource Report Resource Website 50+ mentions |
SNPALYZE (RRID:SCR_009401) | software resource, software application | 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 | 2026-02-13 10:56:24 | 76 | ||||||||||
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ROSATTA SYLLEGO SYSTEM Resource Report Resource Website |
ROSATTA SYLLEGO SYSTEM (RRID:SCR_009363) | Syllego system | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 2, 2014. A genetic data management and analysis system designed to advance your whole genome association, linkage, and eQTL studies, providing you with an easy-to-use project workspace so that you can organize, analyze, and share your genotype and phenotype data along with your analysis results. With the Syllego system, generating high quality analysis data and meaningful results becomes simple. The Syllego system automates all tedious data management and data formatting tasks so that you can streamline your genetic analysis workflows using your analysis methods of choice. Managing all your genetic data and reference information is straightforward. The Syllego system converts public and private genotype data sets and reference annotations, such as dbSNP and HapMap, as well as individual (sample) information into a single, consistent repository for fast, convenient access. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154578 | SCR_009363 | 2026-02-13 10:56:23 | 0 | ||||||||
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ROMPREV Resource Report Resource Website |
ROMPREV (RRID:SCR_009361) | ROMPREV | software resource, software application | Software tool for testing for association between polymorphisms and quantitative traits, as well as estimating trait heritability and locus-specific heritability using family data. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, any with r installation, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154577, biotools:romprev | https://bio.tools/romprev | SCR_009361 | Regression of Offspring on Mid-Parent (REVised) | 2026-02-13 10:56:23 | 0 |
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