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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MINIMAC Resource Report Resource Website 100+ mentions |
MINIMAC (RRID:SCR_009292) | MINIMAC | software resource, software application | 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 | 2026-02-14 02:06:49 | 187 | ||||||
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MFLINK Resource Report Resource Website |
MFLINK (RRID:SCR_009290) | MFLINK | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154477 | SCR_009290 | (nearly) model-free linkage analysis | 2026-02-14 02:07:17 | 0 | |||||||
|
PLABSIM Resource Report Resource Website |
PLABSIM (RRID:SCR_009328) | PLABSIM | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, (aix), linux, ms-windows, (nt) | is listed by: Genetic Analysis Software | nlx_154536 | SCR_009328 | PLAnt Breeding SIMulation | 2026-02-14 02:07:05 | 0 | ||||||||
|
PL-EM Resource Report Resource Website 1+ mentions |
PL-EM (RRID:SCR_009329) | PL-EM | software resource, software application | 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 | 2026-02-14 02:07:18 | 7 | ||||||||
|
PEER Resource Report Resource Website 500+ mentions |
PEER (RRID:SCR_009326) | PEER | software resource, software application | 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 | 2026-02-14 02:06:50 | 553 | |||||||
|
PEDSYS Resource Report Resource Website 1+ mentions |
PEDSYS (RRID:SCR_009324) | PEDSYS | software resource, software application | 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 | 2026-02-14 02:07:05 | 1 | |||||||||
|
PEDVIZAPI Resource Report Resource Website |
PEDVIZAPI (RRID:SCR_009325) | PEDVIZAPI | software resource, software application | A Java Api for the visual analysis of large and complex pedigrees that provides all the necessary functionality for the interactive exploration of extended genealogies. Available packages are mostly focused on a static representation or cannot be added to an existing application; the goal of this open-source library is to provide an application program interface that enables the efficient construction of visual analytic applications for the analysis of family based data. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, r | is listed by: Genetic Analysis Software | nlx_154531 | SCR_009325 | PEDigree VIsualiZation API | 2026-02-14 02:07:18 | 0 | ||||||||
|
MERLIN Resource Report Resource Website 500+ mentions |
MERLIN (RRID:SCR_009289) | MERLIN | software resource, software application | 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 | 2026-02-14 02:07:04 | 910 | ||||||||
|
PED Resource Report Resource Website |
PED (RRID:SCR_009320) | PED | software resource, software application | Powerful pedigree drawing program with two drawing modes: Input mode for fast and automatic drawing; edit mode for text annotations, legends, special symbols. Both input and edit mode provide auto numbering, auto resizing of symbols and fonts, and zooming. PED 4.2a complies with the Recommendations for standardized human pedigree nomenclature. Apart from fully sizeable printed output, pedigrees can be exported as metafiles to virtually any Windows word processor or drawing program. (entry from Genetic Analysis Software) | gene, genetic, genomic, visual smalltalk, ms-windows, (95/98/nt) | is listed by: Genetic Analysis Software | nlx_154514 | SCR_009320 | PEdigree Drawing software | 2026-02-14 02:07:05 | 0 | ||||||||
|
MENDEL Resource Report Resource Website 500+ mentions |
MENDEL (RRID:SCR_009288) | MENDEL | software resource, software application | 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 | 2026-02-14 02:07:11 | 554 | |||||||||
|
PEDAGREE Resource Report Resource Website 1+ mentions |
PEDAGREE (RRID:SCR_009321) | PEDAGREE | software resource, software application | 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) | 2026-02-14 02:07:18 | 1 | ||||||||
|
RELATIVE Resource Report Resource Website 10+ mentions |
RELATIVE (RRID:SCR_009355) | RELATIVE | software resource, software application | 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 | 2026-02-14 02:07:18 | 37 | |||||||||
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RELATIVEFINDER Resource Report Resource Website 1+ mentions |
RELATIVEFINDER (RRID:SCR_009356) | RELATIVEFINDER | software resource, software application | 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 | 2026-02-14 02:06:50 | 2 | |||||||||
|
REAPER Resource Report Resource Website 10+ mentions |
REAPER (RRID:SCR_009354) | REAPER | software resource, software application | 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 | 2026-02-14 02:07:06 | 11 | ||||||||
|
QU-GENE Resource Report Resource Website 1+ mentions |
QU-GENE (RRID:SCR_009351) | QU-GENE | software resource, software application | 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 | 2026-02-14 02:07:18 | 6 | ||||||||
|
RISCALW Resource Report Resource Website |
RISCALW (RRID:SCR_009352) | RISCALW | software resource, software application | Windows program for risk calculation in families with Duchenne muscular dystrophy. It is based on an extended genetic model which includes germline mosaicism and different new mutation rates depending on sex and mutation type. Arbitrary family structures and additional diagnostic information like genotypes from intragenetic and flancing genetic markers of the dystrophin gene, creatin kinase values and female deletion test results can be taken into account. (entry from Genetic Analysis Software) | gene, genetic, genomic, delphi 4, ms-windows | is listed by: Genetic Analysis Software | Duchenne muscular dystrophy | nlx_154567 | SCR_009352 | RISk CALculation in Windows | 2026-02-14 02:06:50 | 0 | |||||||
|
PSEUDOMARKER.M Resource Report Resource Website 1+ mentions |
PSEUDOMARKER.M (RRID:SCR_009346) | PSEUDOMARKER.M | software resource, software application | 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 | 2026-02-14 02:07:18 | 1 | |||||||||
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PSEUDO Resource Report Resource Website 1+ mentions |
PSEUDO (RRID:SCR_009344) | PSEUDO | software resource, software application | 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 | 2026-02-14 02:07:13 | 4 | ||||||||
|
SAS/GENETICS Resource Report Resource Website 100+ mentions |
SAS/GENETICS (RRID:SCR_009343) | SAS/GENETICS | software resource, software application | 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 | 2026-02-14 02:06:50 | 120 | |||||||||
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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 | 2026-02-14 02:07:19 | 0 |
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