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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MLBGH Resource Report Resource Website 1+ mentions |
MLBGH (RRID:SCR_009297) | MLBGH | software application, software resource | Software application that is an extension of the GENEHUNTER program to perform sib-pair and sib-ship linkage analysis using the Maximum Likelihood Binomial (MLB) method. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | nlx_154488 | SCR_009297 | Maximum-Likelihood-Binomial analysis of affected sib-pair and sibship data extended from the GENEHUNTER program | 2026-08-09 09:05:09 | 1 | ||||||||
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MKGST Resource Report Resource Website 1+ mentions |
MKGST (RRID:SCR_009295) | MKGST | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154486 | SCR_009295 | including ASP (power calculator for gene mapping using a sibpair design), with given infants or parent-infant duos), child and putative father), MUTPROF/MUTCOMP (comparison of mutation profiles), Michael Krawczak''s Genetics Software Tools, typed at single locus DNA markers, PATERN (calculation of paternity probabilities from the multilocus DNA profiles of trios, comparing specific types of simple hypotheses regarding the familial relationships involved), ASPSHARE (rapid calculation of the expected ibd sharing at the trait locus, FINDSIRE (identify mothers or sires by means of the comparison of a large number of potential parents, EASYPAT (calculation of likelihood ratios for single locus data, comprising mother, based upon the model) | 2026-08-09 09:05:15 | 2 | ||||||||
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MINIMAC Resource Report Resource Website 100+ mentions |
MINIMAC (RRID:SCR_009292) | MINIMAC | software application, software resource | Software application that is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation. (entry from Genetic Analysis Software) | gene, genetic, genomic |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools is related to: Michigan Imputation Server |
DOI:10.1038/ng.3656 | nlx_154483, OMICS_08953 | https://sources.debian.org/src/minimac4/ | SCR_009292 | MACH | 2026-08-09 09:05:15 | 196 | ||||||
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PL-EM Resource Report Resource Website 1+ mentions |
PL-EM (RRID:SCR_009329) | PL-EM | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154537 | SCR_009329 | Partition-Ligation EM algorithm for haplotype inference with single nucleotide polymorphisms | 2026-08-09 09:05:09 | 7 | ||||||||
|
PEER Resource Report Resource Website 500+ mentions |
PEER (RRID:SCR_009326) | PEER | software application, software resource | Software collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. Applications of PEER have * detected batch effects and experimental confounders * increased the number of expression QTL findings by threefold * allowed inference of intermediate cellular traits, such as transcription factor or pathway activations This project offers an efficient and versatile C++ implementation of the underlying algorithms with user-friendly interfaces to R and python. | gene, genetic, genomic, c++, r, python |
is listed by: Genetic Analysis Software is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:21283789 PMID:20463871 |
nlx_154532, OMICS_04597 | https://github.com/PMBio/peer/wiki | SCR_009326 | 2026-08-09 09:05:09 | 579 | |||||||
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PEDSYS Resource Report Resource Website 1+ mentions |
PEDSYS (RRID:SCR_009324) | PEDSYS | software application, software resource | Full-scale database system developed as a specialized tool for management of genetic, pedigree and demographic data. (entry from Genetic Analysis Software) | gene, genetic, genomic, unix, (sunos, solaris), ms-dos, macos | is listed by: Genetic Analysis Software | nlx_154530 | SCR_009324 | 2026-08-09 09:05:16 | 1 | |||||||||
|
MERLIN Resource Report Resource Website 500+ mentions |
MERLIN (RRID:SCR_009289) | MERLIN | software application, software resource | Software application that carries out single-point and multipoint analyses of pedigree data, including IBD and kinship calculations, nonparametric and variance component linkage analyses, error detection and information content mapping. For multipoint analyses in dense maps, Merlin allows the user to impose constraints on the number of recombinants between consecutive markers. Merlin estimates haplotypes by finding the most likely path of gene flow or by sampling paths of gene flow at all markers jointly. It can also list all possible nonrecombinant haplotypes within short regions. Finally, Merlin provides swap-file support for handling very large numbers of markers as well as gene-dropping simulations for estimating empirical significance levels. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix. linux | is listed by: Genetic Analysis Software | nlx_154475 | SCR_009289 | Multipoint Engine for Rapid Likelihood INference | 2026-08-09 09:04:59 | 931 | ||||||||
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MENDEL Resource Report Resource Website 500+ mentions |
MENDEL (RRID:SCR_009288) | MENDEL | software application, software resource | Software application for genetic analysis of human pedigree data under models involving a small number of loci. MENDEL is useful for segregation analysis, linkage calculations, genetic counseling, allele frequency estimation, and related kinds of problems. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran77 | is listed by: Genetic Analysis Software | nlx_154473 | SCR_009288 | 2026-08-09 09:05:15 | 569 | |||||||||
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PEDAGREE Resource Report Resource Website 1+ mentions |
PEDAGREE (RRID:SCR_009321) | PEDAGREE | software application, software resource | Software program for detecting autosomal marker Mendelian incompatibilities in pedigree data (entry from Genetic Analysis Software) | gene, genetic, genomic, c, c++, unix, linux, ms-windows, ms-dos | is listed by: Genetic Analysis Software | nlx_154515 | SCR_009321 | 1.00 (February 2002) | 2026-08-09 09:05:16 | 1 | ||||||||
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MEGA2 Resource Report Resource Website 100+ mentions |
MEGA2 (RRID:SCR_009286) | MEGA2 | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that uses as input a trio of files: 1) a LINKAGE-format locus file modified to contain locus name information; 2) a LINKAGE-format pedigree file; and 3) a map file. Mega2 then takes this trio of input files and, via a menu-driven interface, transforms them into various other file formats, thus greatly facilitating a variety of different analyses. In addition, for many of these options, it also sets up a C-shell script that then can automatically run these analyses (if you are using Mega2 in a Unix environment that supports C-shell scripts). (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, (solaris, silicon graphics, osf1, macos x), linux, ms-windows, macos, (x) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154471 | SCR_009286 | a Manipulation Environment for Genetic Analyses | 2026-08-09 09:04:59 | 114 | |||||||
|
MAPQTL Resource Report Resource Website 100+ mentions |
MAPQTL (RRID:SCR_009284) | MAPQTL | software application, software resource | Software application for mapping of quantitative trait loci (QTLs) for several types of mapping populations: BC1, F2, RILs, (doubled) haploids, full-sib family of outbreeders. Analyses: interval mapping, composite interval mapping, nonparametric mapping, automatic cofactor selection, permutation test for interval mapping. QTL charts. Everything available in an intuitive MS-Windows user interface. (entry from Genetic Analysis Software) | gene, genetic, genomic, ansi c, delphi, ms-windows, (95/98/me/nt4.0/2000) | is listed by: Genetic Analysis Software | nlx_154468 | SCR_009284 | Software for the calculation of QTL positions on genetic maps | 2026-08-09 09:05:08 | 403 | ||||||||
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MAPMAKER/EXP Resource Report Resource Website 100+ mentions |
MAPMAKER/EXP (RRID:SCR_009281) | MAPMAKER/EXP | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, vms, ms-dos, macos | is listed by: Genetic Analysis Software | nlx_154462 | SCR_009281 | MMDRAWER | 2026-08-09 09:05:08 | 284 | ||||||||
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MAPMAKER/HOMOZ Resource Report Resource Website 1+ mentions |
MAPMAKER/HOMOZ (RRID:SCR_009282) | MAPMAKER/HOMOZ | software application, software resource | Software application that calculates multipoint lod scores in pedigrees with inbreeding loops (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | nlx_154463 | ftp://ftp-genome.wi.mit.edu/distribution/software/homoz | SCR_009282 | homozygosity mapping | 2026-08-09 09:05:15 | 1 | |||||||
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RELATIVE Resource Report Resource Website 10+ mentions |
RELATIVE (RRID:SCR_009355) | RELATIVE | software application, software resource | Software application for relationship estimation, in particular between putative sibs when parents are untyped (entry from Genetic Analysis Software) | gene, genetic, genomic, ansi c, ms-dos, ms-windows, unix | is listed by: Genetic Analysis Software | nlx_154570 | SCR_009355 | 2026-08-09 09:05:10 | 37 | |||||||||
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RELATIVEFINDER Resource Report Resource Website 1+ mentions |
RELATIVEFINDER (RRID:SCR_009356) | RELATIVEFINDER | software application, software resource | 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 | 2026-08-09 09:05:17 | 2 | |||||||||
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REAPER Resource Report Resource Website 10+ mentions |
REAPER (RRID:SCR_009354) | REAPER | software application, software resource | 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 | 2026-08-09 09:05:01 | 11 | ||||||||
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QU-GENE Resource Report Resource Website 1+ mentions |
QU-GENE (RRID:SCR_009351) | QU-GENE | software application, software resource | 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 | 2026-08-09 09:05:00 | 6 | ||||||||
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PSEUDOMARKER.M Resource Report Resource Website 1+ mentions |
PSEUDOMARKER.M (RRID:SCR_009346) | PSEUDOMARKER.M | software application, software resource | 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 | 2026-08-09 09:05:17 | 1 | |||||||||
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PSEUDO Resource Report Resource Website 1+ mentions |
PSEUDO (RRID:SCR_009344) | PSEUDO | software application, software resource | 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 | 2026-08-09 09:05:00 | 4 | ||||||||
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SAS/GENETICS Resource Report Resource Website 100+ mentions |
SAS/GENETICS (RRID:SCR_009343) | SAS/GENETICS | software application, software resource | 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 | 2026-08-09 09:05:17 | 120 |
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