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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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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PASS PEDIGREE Resource Report Resource Website |
PASS PEDIGREE (RRID:SCR_009315) | PASS PEDIGREE | software resource, software application | Software application to draw the most complex family trees in a matter of minutes instead of hours of work. The basis of this is an algorithm for automatically builing a family tree. Of course, manual adjustments in the family tree can be made for your specific requirements. PASS Pedigree meets all international conventions concerning the drawing of pedigrees. A converter can convert historical Cyrillic pedigrees automatically to PASS Pedigree. Unlike before, all your family trees are stored in one single database. PASS Pedigree can intelligently connect to many genetic centers (e.g. three genetic centers in the Netherlands) with the existing patient information, via the lab system HELIX based on HL7 techniques. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154509 | SCR_009315 | 2026-02-13 10:56:22 | 0 | |||||||||
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OSIRIS Resource Report Resource Website 100+ mentions |
OSIRIS (RRID:SCR_009313) | OSIRIS | software resource, software application | Software tool for the retrieval of articles from MEDLINE related to the sequence variants reported for a human gene. The variations considered are single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (indel), microsatellite, and named variations (e.g. Alu sequences). (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154505 | SCR_009313 | 2026-02-13 10:56:23 | 218 | ||||||||
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P ACT Resource Report Resource Website 1+ mentions |
P ACT (RRID:SCR_009314) | P_ACT | software resource, software application | An R program that adjusts sets of up to 1000 p-values from association tests between correlated traits and SNPs for multiple testing, accounting for the correlation between tests. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154506 | SCR_009314 | P-values: Adjustment for Correlated Tests | 2026-02-13 10:56:22 | 4 | ||||||||
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NOCOM Resource Report Resource Website 1+ mentions |
NOCOM (RRID:SCR_009310) | NOCOM | software resource, software application | Software application to estimate parameters for mixture of normal distributions (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran, ms-dos, os2 | is listed by: Genetic Analysis Software | nlx_154500 | SCR_009310 | 2026-02-13 10:56:22 | 8 | |||||||||
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SMOOTH Resource Report Resource Website 50+ mentions |
SMOOTH (RRID:SCR_009398) | software resource, software application | Software tool that recognises and removes the most unrealistic data pointsfor the construction of accurate linkage maps, which is not so much depending on the quality of the mapping software, but mostly on the marker data quality. Missing values and scoring errors can severely influence the calculated marker order. This software was used to construct the 10,000 marker potato map. The removal of improbable data point is a good medicine for linkage maps, that is not easily overdosed. One error is more harmfull than ten missing values. The software was never intended as user-friendly software. In these days it would be more useful to re-do the programming of the pascal source code into a perl script. Anyone who takes the initiative to generate such a script is welcomed to contact the authors. SMOOTH works best in close cooperation with mapping algorithm RECORD (entry from Genetic Analysis Software) | gene, genetic, genomic, pascal, ms-dos | is listed by: Genetic Analysis Software | nlx_154636 | http://www.plantbreeding.wur.nl/UK/software_smooth.html | SCR_009398 | 2026-02-13 10:56:24 | 57 | |||||||||
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SIMULATE Resource Report Resource Website 10+ mentions |
SIMULATE (RRID:SCR_009391) | software resource, software application | Software program to simulate genotypes in family members for a map of linked markers unlinked to a given affection status locus. the output is ready for analysis with UNKNOWN, ISIM, LSIM, or MSIM of the SLINK package. (entry from Genetic Analysis Software) | gene, genetic, genomic, pascal, ms-dos, vms, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154630, biotools:simulate | https://bio.tools/simulate | SCR_009391 | 2026-02-13 10:56:24 | 11 | |||||||||
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SIMUPOP Resource Report Resource Website 10+ mentions |
SIMUPOP (RRID:SCR_009392) | software resource, software application | A forward-based population genetics simulation program capable of simulating very complex evolution processes on large (think of millions) populations. Major features include variable population size; many built-in and hybrid (write in python) mutation, migration, selection models. simuPOP can be extended in Python so there is no limit on what you can do with it. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, (provided as python libraries) | is listed by: Genetic Analysis Software | nlx_154631 | https://pypi.python.org/pypi/simuPOP | http://bp6.stat.rice.edu:8080/simuPOP/ | SCR_009392 | 2026-02-13 10:56:24 | 26 | ||||||||
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MULTISIM Resource Report Resource Website 10+ mentions |
MULTISIM (RRID:SCR_009308) | MULTISIM | software resource, software application | Software application to analyze the numbers of individuals that founded new populations following a bottleneck or founding event (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-dos | is listed by: Genetic Analysis Software | nlx_154498 | SCR_009308 | 2026-02-13 10:56:23 | 12 | |||||||||
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TFPGA Resource Report Resource Website 50+ mentions |
TFPGA (RRID:SCR_009421) | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software program that calculates descriptive statistics, genetic distances, and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, exact tests for genetic differentiation, Mantel tests, and UPGMA cluster analyses. (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154680 | SCR_009421 | Tools For Population Genetic Analyses | 2026-02-13 10:56:25 | 57 |
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