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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PEDMANAGER Resource Report Resource Website |
PEDMANAGER (RRID:SCR_009300) | PEDMANAGER | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | nlx_154491 | SCR_009300 | 2026-02-15 09:20:00 | 0 | |||||||||
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SIMLINK Resource Report Resource Website 1+ mentions |
SIMLINK (RRID:SCR_009387) | software application, software resource | Software program to estimate the probability (power) of detecting linkage given family history information on a set of identified pedigrees. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran, ms-dos, unix, sunos, vms | is listed by: Genetic Analysis Software | nlx_154625 | SCR_009387 | 2026-02-15 09:20:02 | 3 | ||||||||||
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SIMLA Resource Report Resource Website 1+ mentions |
SIMLA (RRID:SCR_009385) | software application, software resource | SIMulation program that generates data sets of families for use in Linkage and Association studies. It allows the user flexibility in specifying marker and disease placement, locus heterogeneity, disequilibrium between markers and between markers and disease loci. Output is in the form of a LINKAGE pedigree file and is easily utilized, either directly or with minimal reformatting, as input for various genetic analysis packages (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, solaris, linux | is listed by: Genetic Analysis Software | nlx_154623 | http://wwwchg.duhs.duke.edu/software/simla.html | SCR_009385 | SIMulation of pedigree data for Linkage and Association studies | 2026-02-15 09:20:11 | 1 | ||||||||
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SILCLOD Resource Report Resource Website |
SILCLOD (RRID:SCR_009383) | software application, software resource | Software application to calculate nominal significance levels and critical LOD scores depending on the length of the investigated region, number of chromosomes, and the cross-over rate. The global significance level as well as the precision of the calculation have to be specified. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154619 | http://www.imbs.uni-luebeck.de/pub/silcLOD/index.html | SCR_009383 | SIgnificance Levels and Critical LODs | 2026-02-15 09:20:02 | 0 | ||||||||
|
SIBERROR Resource Report Resource Website |
SIBERROR (RRID:SCR_009380) | software application, software resource | Software application that identifies pedigree errors in sibship data. Examples include half siblings, unrelated individuals, identical twins, and parental exclusions. The test statistic is based on the summation of the number of alleles shared by a pair of relatives for a large number of markers and the number of alleles and allele frequencies for those markers. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | nlx_154615 | SCR_009380 | SibError | 2026-02-15 09:19:43 | 0 | |||||||||
|
TAGGER Resource Report Resource Website 50+ mentions |
TAGGER (RRID:SCR_009419) | software application, software resource | 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 | 2026-02-15 09:20:11 | 91 | ||||||||||
|
SPLINK Resource Report Resource Website 10+ mentions |
SPLINK (RRID:SCR_009414) | software application, software resource | 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 | 2026-02-15 09:19:43 | 46 | ||||||||
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SSAHASNP Resource Report Resource Website 1+ mentions |
SSAHASNP (RRID:SCR_009415) | SSAHASNP | software application, software resource | 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 | 2026-02-15 09:20:11 | 4 | ||||||||
|
SPIP Resource Report Resource Website 100+ mentions |
SPIP (RRID:SCR_009410) | software application, software resource | 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 | 2026-02-15 09:19:43 | 423 | |||||||||
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SPLAT Resource Report Resource Website 10+ mentions |
SPLAT (RRID:SCR_009411) | SPLAT | software application, software resource | 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 | 2026-02-15 09:20:11 | 19 | |||||||
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PLABQTL Resource Report Resource Website 10+ mentions |
PLABQTL (RRID:SCR_012789) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154535 | SCR_012789 | PLAnt Breeding QTL analysis | 2026-02-15 09:20:38 | 14 | |||||||||
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HAPBLOCK 2 Resource Report Resource Website |
HAPBLOCK 2 (RRID:SCR_012788) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, stata | is listed by: Genetic Analysis Software | nlx_154376 | SCR_012788 | 2026-02-15 09:20:21 | 0 | ||||||||||
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SPERM Resource Report Resource Website 10+ mentions |
SPERM (RRID:SCR_009409) | software application, software resource | 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 | 2026-02-15 09:20:02 | 16 | |||||||||
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SNPALYZE Resource Report Resource Website 50+ mentions |
SNPALYZE (RRID:SCR_009401) | software application, software resource | 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 | 2026-02-15 09:20:11 | 76 | ||||||||||
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SMOOTH Resource Report Resource Website 50+ mentions |
SMOOTH (RRID:SCR_009398) | software application, software resource | 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 | 2026-02-15 09:20:07 | 57 | |||||||||
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SIMULATE Resource Report Resource Website 10+ mentions |
SIMULATE (RRID:SCR_009391) | software application, software resource | 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 | 2026-02-15 09:20:02 | 11 | |||||||||
|
SIMUPOP Resource Report Resource Website 10+ mentions |
SIMUPOP (RRID:SCR_009392) | software application, software resource | 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 | 2026-02-15 09:19:43 | 26 | ||||||||
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WHAIT Resource Report Resource Website |
WHAIT (RRID:SCR_009425) | 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 | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154691 | SCR_009425 | Weighted Haplotype test And an Imputation-based Test. | 2026-02-15 09:20:08 | 0 | ||||||||
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ZAPLO Resource Report Resource Website 1+ mentions |
ZAPLO (RRID:SCR_009426) | ZAPLO | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. | gene, genetic, genomic, linux, unix, solaris | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154692 | SCR_009426 | 2026-02-15 09:20:02 | 3 | ||||||||
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UNKNOWN Resource Report Resource Website 10+ mentions |
UNKNOWN (RRID:SCR_009423) | UNKNOWN | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154684 | SCR_009423 | LINKAGE - general pedigrees | 2026-02-15 09:19:43 | 13 |
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