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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SIMLA Resource Report Resource Website 1+ mentions |
SIMLA (RRID:SCR_009385) | software resource, software application | 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 | 2026-02-14 02:07:13 | 1 | ||||||||
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SILCLOD Resource Report Resource Website |
SILCLOD (RRID:SCR_009383) | software resource, software application | 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 | 2026-02-14 02:07:19 | 0 | ||||||||
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SIBERROR Resource Report Resource Website |
SIBERROR (RRID:SCR_009380) | software resource, software application | 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 | 2026-02-14 02:06:51 | 0 | |||||||||
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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 | 2026-02-14 02:07:08 | 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 | 2026-02-14 02:07:14 | 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 | 2026-02-14 02:07:07 | 4 | ||||||||
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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 | 2026-02-14 02:07:07 | 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 | 2026-02-14 02:07:19 | 19 | |||||||
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PLABQTL Resource Report Resource Website 10+ mentions |
PLABQTL (RRID:SCR_012789) | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154535 | SCR_012789 | PLAnt Breeding QTL analysis | 2026-02-14 02:07:10 | 14 | |||||||||
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HAPBLOCK 2 Resource Report Resource Website |
HAPBLOCK 2 (RRID:SCR_012788) | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, stata | is listed by: Genetic Analysis Software | nlx_154376 | SCR_012788 | 2026-02-14 02:07:16 | 0 | ||||||||||
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TOMCAT Resource Report Resource Website 10+ mentions |
TOMCAT (RRID:SCR_013120) | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May24,2023. Software program that implements the Mantel statistics as proposed by Beckmann et al. (2005) to test for association between genetic markers and phenotypes in case-control studies using haplotype information. The potential value of haplotypes has attracted widespread interest in the mapping of complex traits. Haplotype sharing methods take into account linkage disequilibrium information between multiple markers, and may have good power to detect predisposing genes. We present a new approach based on Mantel statistics for space time clustering, which we developed in order to improve the power of haplotype sharing analysis for gene mapping in complex disease. The new statistic correlates genetic similarity and phenotypic similarity across pairs of haplotypes for case-only and case-control studies. The genetic similarity is measured as the shared length between haplotypes around a putative disease locus. Alternative measures for the phenotypic similarity were implemented. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, 5.0 | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154681 | SCR_013120 | 2026-02-14 02:07:22 | 18 | |||||||||
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SCORE-SEQ Resource Report Resource Website 1+ mentions |
SCORE-SEQ (RRID:SCR_013121) | software resource, software application | A command-line program for detecting disease associations with rare variants in sequencing studies. The mutation information is aggregated across multiple variant sites of a gene through a weighted linear combination and then related to disease phenotypes through appropriate regression models. The weights can be constant or dependent on allele frequencies and phenotypes. The association testing is based on score-type statistics. The allele-frequency threshold can be fixed or variable. Statistical significance can be assessed by using asymptotic normal approximation or resampling. The current release covers binary and continuous traits with arbitrary covariates under case-control and cross-sectional sampling. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154611 | SCR_013121 | SCORE-type tests for detecting disease associations with rare variants in SEQuencing Studies | 2026-02-14 02:06:54 | 6 | |||||||||
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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 | 2026-02-14 02:07:14 | 16 | |||||||||
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WHAIT Resource Report Resource Website |
WHAIT (RRID:SCR_009425) | software resource, software application | 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. | 2026-02-14 02:07:20 | 0 | ||||||||
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ZAPLO Resource Report Resource Website 1+ mentions |
ZAPLO (RRID:SCR_009426) | ZAPLO | software resource, software application | 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 | 2026-02-14 02:06:52 | 3 | ||||||||
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UNKNOWN Resource Report Resource Website 10+ mentions |
UNKNOWN (RRID:SCR_009423) | UNKNOWN | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154684 | SCR_009423 | LINKAGE - general pedigrees | 2026-02-14 02:07:14 | 13 | ||||||||
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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 | 2026-02-14 02:07:20 | 57 | ||||||||
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ENDOG Resource Report Resource Website 100+ mentions |
ENDOG (RRID:SCR_013289) | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software application that calculates individual inbreeding (F) and average relatedness (AR) coefficients. Additionally, users can compute useful parameters in population genetics such as: the number of ancestors explaining genetic variability; the genetic importance of the herds; F statistics from genealogical information. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran 77 | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154299 | SCR_013289 | 2026-02-14 02:06:54 | 120 | |||||||||
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WEIGHTED FDR Resource Report Resource Website |
WEIGHTED FDR (RRID:SCR_013442) | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154604, SCR_000848, nlx_154690, biotools:weighted_fdr | https://bio.tools/weighted_fdr | SCR_013442 | R/WEIGHTED_FDR | 2026-02-14 02:07:18 | 0 | ||||||||
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MENDELSOFT Resource Report Resource Website |
MENDELSOFT (RRID:SCR_013177) | software resource, software application | Software application for identifying all Mendelian inconsistencies in complex pedigree data with thousand of individuals, including many loops and several errors. Can also infer missing genotypes. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, linux/cygwin, ms-windows, macos | is listed by: Genetic Analysis Software | nlx_154474 | SCR_013177 | 2026-02-14 02:07:11 | 0 |
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