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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BPPH Resource Report Resource Website |
BPPH (RRID:SCR_009136) | BPPH | software resource, software application | Software application for inferring haplotypes from genotypes to determine if there are resulting haplotypes that fit a tree model (i.e. a perfect phylogeny, a coalescent). In population genetic terms, BPPH determines whether a set of SNP genotypes can be explained by haplotype pairs that could have evolved on a coalescent under the no-recombination, infinite sites model. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154251 | SCR_009136 | Berkeley method for Perfect Phylogeney Haplotyping | 2026-02-14 02:06:59 | 0 | ||||||||
|
BLOCK Resource Report Resource Website 100+ mentions |
BLOCK (RRID:SCR_009133) | BLOCK | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that performs general pedigree analysis on a general pedigree with any number of loops. It also allows users to perform two-point linkage analysis on a general pedigree with an arbitrary number of alleles., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, ms-dos, linux, unix, solaris, irix 64, aix 3.2.5, dec alpha | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154247 | SCR_009133 | Blocking Gibbs sampler for pedigree analysis | 2026-02-14 02:07:13 | 134 | |||||||
|
QUTIE Resource Report Resource Website 1+ mentions |
QUTIE (RRID:SCR_009098) | QUTIE | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application for enabling the analysis of rare variants in large-scale case control and quantitative trait association studies. CCRaVAT (Case-Control Rare Variant Analysis Tool) and QuTie (Quantitative Trait) are software packages that enable efficient large-scale analysis of rare variants across specific regions or genome-wide. These programs implement a rare variant super-locus or collapsing method that investigates the accumulation of rare variant alleles in either a case-control or quantitative trait study design. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154191 | SCR_009098 | Case-Control RAre Variant Analysis Tool CCRAVAT | 2026-02-14 02:07:07 | 1 | |||||||
|
BLADE Resource Report Resource Website 100+ mentions |
BLADE (RRID:SCR_009132) | BLADE | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154246 | SCR_009132 | Bayesian LinkAge DisEquilibrium mapping | 2026-02-14 02:06:59 | 113 | ||||||||
|
STEPC Resource Report Resource Website |
STEPC (RRID:SCR_009096) | STEPC | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154114 | SCR_009096 | STatistical Explanation for Positional Cloning | 2026-02-14 02:07:13 | 0 | |||||||
|
RECORD Resource Report Resource Website 1000+ mentions |
RECORD (RRID:SCR_009097) | RECORD | software resource, software application | Software application that can be used for the ordering of loci on genetic linkage maps. The method is based on minimisation of the total number of recombination events. Since the criterion does not require intensive calculations, the algorithm rapidly produces an optimal ordering as well as a series of near-optimal ones. The latter provides insight into the local certainty of ordering along the map. RECORD can deal with the following types of mapping populations: BC1, F2, F3, RILs (in fact any generation obtained by repeated selfing of a hybrid between homozygous parents). Data files are .LOC JoinMap format. Mapping populations from non-inbreds should be split into BC1 or HAP data that represent the maternal and paternal gametes. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows, (win98, xp) and ms-dos | is listed by: Genetic Analysis Software | nlx_154153 | SCR_009097 | REcombination Counting and ORDering | 2026-02-14 02:06:44 | 1321 | ||||||||
|
TDT-AE Resource Report Resource Website 1+ mentions |
TDT-AE (RRID:SCR_009094) | TDT-AE | software resource, software application | Software program that computes a likelihood-based transmission disequilibrium test. The data are genotypes on trios (father, mother, affected child) in which random genotyping errors leading to Mendelian inconsistencies may or may not have occurred. This program computes the TDT-AE statistic on all trios (whether Mendelianly consistent or not) and thereby maintains a correct type I error rate in the presence of random genotyping errors. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, ms-windows, (2000/dos), unix, (sun solaris), linux, (redhat) | is listed by: Genetic Analysis Software | PMID:11443542 | nlx_154112 | ftp://linkage.rockefeller.edu/software/tdtae2 | SCR_009094 | Transmission Disequilibrium Test Allowing for Errors | 2026-02-14 02:07:07 | 2 | ||||||
|
GENOMIZER Resource Report Resource Website 1+ mentions |
GENOMIZER (RRID:SCR_009127) | GENOMIZER | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. A platform independent Java program for the analysis of genome wide association experiments. (entry from Genetic Analysis Software). | gene, genetic, genomic, java, ms-windows, linux | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154349 | http://www.ikmb.uni-kiel.de/genomizer/ | SCR_009127 | 2026-02-14 02:07:08 | 3 | |||||||
|
GENEPOOL Resource Report Resource Website 10+ mentions |
GENEPOOL (RRID:SCR_009087) | GENEPOOL | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that provides analysis tools for the detection of shifts in relative allele frequency between pooled genomic DNA from cases and controls using SNP-based genotyping microarrays. GenePool supports genotyping platforms from Affymetrix and Illumina. | gene, genetic, genomic, c/c++/perl, linux, macos, (should compile on most unix systems with gcc) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154104 | SCR_009087 | 2026-02-14 02:07:13 | 48 | ||||||||
|
ANALYZE Resource Report Resource Website 1000+ mentions |
ANALYZE (RRID:SCR_009120) | ANALYZE | software resource, software application | A set of useful accessory programs to the LINKAGE package. It simplifies the performance of a large array of parametric and nonparametric tests for linkage and association on data entered in LINKAGE format pedigree and parameter files. (entry from Genetic Analysis Software) | gene, genetic, genomic, pascal, unix, sunos, solaris, osf1 |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154223 | SCR_009120 | 2026-02-14 02:07:13 | 1102 | |||||||||
|
EPISTACY Resource Report Resource Website 1+ mentions |
EPISTACY (RRID:SCR_009088) | EPISTACY | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, sas | is listed by: Genetic Analysis Software | nlx_154105 | SCR_009088 | 2026-02-14 02:06:44 | 1 | |||||||||
|
R/QTL Resource Report Resource Website 500+ mentions |
R/QTL (RRID:SCR_009085) | R/QTL | software resource, software application | Software program for mapping quantitative trait loci in experimental crosses. (entry from Genetic Analysis Software) | gene, genetic, genomic, c and r, unix, ms-windows, macos |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
DOI:10.1093/bioinformatics/btg112 | OMICS_07093, nlx_154097 | https://sources.debian.org/src/r-cran-qtl/ | SCR_009085 | 2026-02-14 02:07:07 | 987 | |||||||
|
QUANTO Resource Report Resource Website 500+ mentions |
QUANTO (RRID:SCR_009084) | QUANTO | software resource, software application | Software program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs. Quanto is a 32-bit Windows application requiring Windows 95, 98, NT, 2000, ME or XP to run. The graphical user interface allows th e user to easily change the model and view the results without having to edit an input file and rerun the program for every model. The results of a session are stored to a log file. This log can be printed or saved to a file for reviewing at a later date. An option is included to create a text file of the log that can be imported into other documents. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows, (98/nt/2000/..) |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154095 | SCR_009084 | 2026-02-14 02:06:44 | 915 | |||||||||
|
BOTTLENECK Resource Report Resource Website 100+ mentions |
BOTTLENECK (RRID:SCR_009082) | BOTTLENECK | software resource, software application | Software application for detecting recent effective population size reductions from allele data frequencies (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows, (95) | is listed by: Genetic Analysis Software | nlx_154093 | SCR_009082 | 2026-02-14 02:06:58 | 486 | |||||||||
|
SQTDT/SPDT Resource Report Resource Website |
SQTDT/SPDT (RRID:SCR_009080) | SQTDT/SPDT | software resource, software application | Software application for semiparametric family-based association (entry from Genetic Analysis Software) | gene, genetic, genomic, linux | is listed by: Genetic Analysis Software | nlx_154091 | SCR_009080 | 2026-02-14 02:06:44 | 0 | |||||||||
|
DGENE Resource Report Resource Website 1+ mentions |
DGENE (RRID:SCR_009158) | DGENE | software resource, software application | THIS RESOURCE IS NO LOGER IN SERVICE. Documented on May 16,2023. A simple dBASE III program for the management of pedigree and locus data. It permits easy extraction of genetic data for use with MENDEL and FISHER. (entry from Genetic Analysis Software) | gene, genetic, genomic, dbase iii, ms-dos | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LOGER IN SERVICE | nlx_154281 | SCR_009158 | 2026-02-14 02:07:08 | 5 | ||||||||
|
COPE Resource Report Resource Website 500+ mentions |
COPE (RRID:SCR_009153) | COPE | software resource, software application | Software application that includes a Java program for drawing pedigrees and a standardized system for pedigree storage. Unlike other existing pedigree programs, this software is particularly intended for epidemiologists in the sense that it allows customized automatic drawing of large numbers of pedigrees and remote and distributed consultation of pedigrees. (entry from Genetic Analysis Software) | gene, genetic, genomic, java |
is listed by: Genetic Analysis Software is parent organization of: COPE: Cytokines and Cells Online Pathfinder Encyclopaedia |
nlx_154274 | SCR_009153 | COllaborative Pedigree drawing Environment | 2026-02-14 02:06:59 | 841 | ||||||||
|
CHROMOSCAN Resource Report Resource Website 1+ mentions |
CHROMOSCAN (RRID:SCR_009151) | CHROMOSCAN | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that is an implementation of a genome-based scan statistic that detects genomic regions. | gene, genetic, genomic, java | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154270 | http://www.epidkardia.sph.umich.edu/software/chromoscan/ | SCR_009151 | 2026-02-14 02:06:45 | 2 | |||||||
|
CHIAMO Resource Report Resource Website 1+ mentions |
CHIAMO (RRID:SCR_009150) | CHIAMO | software resource, software application | Software application for calling genotypes from the Affymetrix 500K Mapping chip. The program allows for multiple cohorts which have potentially different intensity characteristics that can lead to elevated false-positive rates in genome-wide studies. The underlying model has a hierarchical structure that allows for correlation between the parameters of each cohort. The output files produced by CHIAMO feed directly into both the programs SNPTEST and IMPUTE. CHIAMO was used to call genotypes for the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC). | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154269 | http://www.stats.ox.ac.uk/~marchini/software/gwas/chiamo.html | SCR_009150 | 2026-02-14 02:07:14 | 2 | ||||||||
|
CHECKMATRIX Resource Report Resource Website 1+ mentions |
CHECKMATRIX (RRID:SCR_009149) | CHECKMATRIX | software resource, software application | Software application that serves as a visualization tool to validate constructed genetic maps. CheckMatrix generates graphical genotypes and two-dimensional heat plots of pairwise scores. Visualization of regions with positive and negative linkage as well as of allele fraction per marker simplifies genetic map validation without applying statistical approaches. CheckMatrix works in conjunction with MadMapper and freely available at http://www.atgc.org/XLinkage/MadMapper/ (entry from Genetic Analysis Software) | gene, genetic, genomic, python | is listed by: Genetic Analysis Software | nlx_154268 | SCR_009149 | PY_MATRIX_D | 2026-02-14 02:06:59 | 9 |
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