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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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WEBQTL Resource Report Resource Website 10+ mentions |
WEBQTL (RRID:SCR_009072) | WEBQTL | software application, software resource | An interactive web site useful for exploring the genetic modulation of thousands of phenotypes gathered over a 30-year period by hundreds of investigators using reference panels of recombinant inbred strains of mice. WebQTL includes dense error-checked genetic maps, as well as extensive gene expression data sets (Affymetrix) acquired across more than 35 strains of mice. WebQTL accepts user-entered traits for BXD, AXB/BXA, CXB, BXH, AKXD recombinant inbred strains. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, and, python, all via internet | is listed by: Genetic Analysis Software | nlx_154066 | http://www.webqtl.org/search.html | SCR_009072 | 2026-08-09 09:05:08 | 46 | ||||||||
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genehunter-imprinting Resource Report Resource Website 1+ mentions |
genehunter-imprinting (RRID:SCR_009104) | GENEHUNTER-TWOLOCUS | software application, software resource | Resource no longer in service. Documented on February 23,2021.Software tool as modification of GENEHUNTER software package . Allows for parametric multi-marker linkage analysis of dichotomous traits caused by imprinted genes. By specification of two heterozygote penetrance parameters, paternal and maternal origin of the disease allele can be treated differently in terms of probability of expression of the trait. | gene, genetic, genomic, c, unix, sunos, solaris, osf, hpux, aix, ultrix, linux, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
DOI:10.1086/302911 | Resource no longer in service. Documented on February 23,2021 | nlx_154199, biotools:genehunter-imprinting | https://bio.tools/genehunter-imprinting | http://www.staff.uni-marburg.de/~strauchk/software.html | SCR_009104 | GENEHUNTER-MODSCORE, GENEHUNTER-PLUS, GENEHUNTER, GENEHUNTER-IMPRINTING | 2026-08-09 09:05:08 | 1 | ||||
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GENEHUNTER-MODSCORE Resource Report Resource Website 1+ mentions |
GENEHUNTER-MODSCORE (RRID:SCR_009069) | GENEHUNTER-MODSCORE | software application, software resource | Software application that is an extension of GENEHUNTER-IMPRINTING, based on the original GENEHUNTER version 2.1 release 6, that allows for a MOD-score analysis, in which parametric LOD scores are maximized over the parameters of the trait model, i.e., the penetrances and disease allele frequency. As of version 2.0, it is possible to use sex-specific recombination frequencies. The genetic positions of markers can be automatically read from a publicly available genetic map. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, sunos, solaris, osf, hpux, aix, ultrix, linux, ms-windows | is listed by: Genetic Analysis Software | nlx_154061 | http://www.staff.uni-marburg.de/~strauchk/software.html | SCR_009069 | 2026-08-09 09:05:07 | 1 | ||||||||
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MAREYMAP Resource Report Resource Website 10+ mentions |
MAREYMAP (RRID:SCR_009066) | MAREYMAP | software application, software resource | Software application that is a meiotic recombination rate estimation program. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, tcl/tk | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154056 | SCR_009066 | 2026-08-09 09:05:07 | 41 | ||||||||
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ASSOCIATIONVIEWER Resource Report Resource Website |
ASSOCIATIONVIEWER (RRID:SCR_009063) | ASSOCIATIONVIEWER | software application, software resource | A Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154050, biotools:association_viewer | https://bio.tools/association_viewer | SCR_009063 | 2026-08-09 09:05:07 | 0 | ||||||||
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WHICHRUN Resource Report Resource Website |
WHICHRUN (RRID:SCR_009064) | WHICHRUN | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that uses multilocus genotypic data to allocate individuals to their most likely source population. | gene, genetic, genomic, c++, ms-windows, (95/98/nt) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154051 | http://www.bml.ucdavis.edu/whichrun.htm | SCR_009064 | 2026-08-09 09:04:56 | 0 | |||||||
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MAP MANAGER QTX Resource Report Resource Website 1+ mentions |
MAP MANAGER QTX (RRID:SCR_009061) | MAP MANAGER QTX | software application, software resource | A graphic, interactive program to map quantitative trait loci using intercrosses, backcrosses or recombinant inbred strains in experimental plants or animals. A completely rewritten cross-platform version of Map Manager QT with enhanced analysis functions. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, and cross-platform code from xvt, ms-windows, macos | is listed by: Genetic Analysis Software | nlx_154046 | SCR_009061 | 2026-08-09 09:04:56 | 4 | |||||||||
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G-MENDEL Resource Report Resource Website |
G-MENDEL (RRID:SCR_009062) | G-MENDEL | software application, software resource | Software tool for construction of genetic linkage maps and analyzing Mendelian phenotypes. (entry from Genetic Analysis Software) | gene, genetic, genomic, unix, ms-windows | is listed by: Genetic Analysis Software | nlx_154049 | http://cropandsoil.oregonstate.edu/G-mendel | SCR_009062 | 2026-08-09 09:05:04 | 0 | ||||||||
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BQTL Resource Report Resource Website 1+ mentions |
BQTL (RRID:SCR_009137) | BQTL | software application, software resource | Software application for the mapping of genetic traits from line crosses and recombinant inbred lines. It performs (1) maximum likelihood estimation of multi-gene models; (2) Bayesian estimation of multi-gene models via Laplace Approximations; and (3) interval mapping and composite interval mapping of genetic loci (entry from Genetic Analysis Software) | gene, genetic, genomic, s, c, fortran, the software is engineered to work in conjunction with r., unix, ms-windows, macos | is listed by: Genetic Analysis Software | nlx_154252 | http://hacuna.ucsd.edu/bqtl/ | SCR_009137 | Bayesian Quantitative Trait Locus mapping | 2026-08-09 09:05:10 | 1 | |||||||
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DNABASER Resource Report Resource Website 10+ mentions |
DNABASER (RRID:SCR_009138) | DNABASER | software application, software resource | Software tool for manual and automatic DNA sequence assembly, DNA sequence analysis, automatic sample processing, contig editing, metadata integration, file format conversion and mutation detection. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154256 | SCR_009138 | 2026-08-09 09:04:57 | 45 | ||||||||
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BPPH Resource Report Resource Website |
BPPH (RRID:SCR_009136) | BPPH | software application, software resource | 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 | 2026-08-09 09:05:06 | 0 | ||||||||
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BLOCK Resource Report Resource Website 100+ mentions |
BLOCK (RRID:SCR_009133) | BLOCK | software application, software resource | 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 | 2026-08-09 09:05:06 | 134 | |||||||
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FastTree Resource Report Resource Website 5000+ mentions |
FastTree (RRID:SCR_015501) | source code, software resource | Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution. | phylogenetic tree, phylogenetic tree creation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: VeryFastTree |
PMID:19377059 DOI:10.1371/journal.pone.0009490 |
biotools:fasttree, OMICS_14703 | https://bio.tools/fasttree, https://sources.debian.org/src/fasttree/ | SCR_015501 | 2026-08-09 09:06:25 | 6279 | ||||||||
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MSM Resource Report Resource Website 1+ mentions |
MSM (RRID:SCR_015500) | source code, software resource | Source code for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal data. It was originally designed for processes observed at arbitrary times in continuous time but some other observation schemes are supported. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates, which may be constant or piecewise-constant in time. | markov, continuous time markov, hidden markov multi state model | is hosted by: CRAN | DOI:10.18637/jss.v038.i08 | Available for download | https://www.jstatsoft.org/article/view/v038i08 | SCR_015500 | Multi-State Markov and Hidden Markov Models in Continuous Time (MSM), Multi-State Markov and Hidden Markov Models in Continuous Time | 2026-08-09 09:06:53 | 1 | |||||||
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phytools Resource Report Resource Website 500+ mentions |
phytools (RRID:SCR_015502) | source code, software resource | Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species. | r package, phylogenetic comparison, phylogenetic analysis |
is listed by: Debian is listed by: OMICtools is hosted by: GitHub |
DOI:10.1111/j.2041-210X.2011.00169.x | Available for download, Acknowledgement requested | OMICS_12499 | https://github.com/liamrevell/phytools, https://sources.debian.org/src/r-cran-phytools/ | SCR_015502 | 2026-08-09 09:06:41 | 718 | |||||||
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Mikado Resource Report Resource Website 50+ mentions |
Mikado (RRID:SCR_016159) | source code, software resource | Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus. | annotation, rna-seq, genomics, transcriptomics | is related to: Portcullis | BBSRC BB/J004669/1; BBSRC BB/J010375/1; BBSRC BB/CSP17270/1; BBSRC BB/CCG1720/1 |
DOI:10.1101/216994 | Free, Available for download | http://mikado.readthedocs.io/ | SCR_016159 | 2026-08-09 09:06:59 | 93 | |||||||
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CUDAICA Resource Report Resource Website 1+ mentions |
CUDAICA (RRID:SCR_015630) | source code, software resource | Software that implements Infomax ICA, which is an algorithm to perform Independent Component Analysis, in CUDA (a parallel computing platform and programming model). | infomax ica, ica, independent component analysis, eeg | PMID:22811699 | Free, Available for download | https://liaa.dc.uba.ar/node/10 | SCR_015630 | 2026-08-09 09:06:27 | 3 | |||||||||
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regist custom genome Resource Report Resource Website 1+ mentions |
regist custom genome (RRID:SCR_015999) | source code, software resource | One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide.. Regist custom genome software registers custom genomes to Genome Explorer (IN: FASTA). | analysis, pipeline, maser, genome, explorer, fasta, custom, register | Ministry of Education ; Culture ; Sports ; Science and Technology ; Japan |
Restricted | http://cell-innovation.nig.ac.jp/maser_cgi/cip-pl_list_violin_en.cgi | SCR_015999 | Management and Analysis System for Enormous Reads: regist custom genome | 2026-08-09 09:06:33 | 1 | ||||||||
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kCSD-python Resource Report Resource Website 1+ mentions |
kCSD-python (RRID:SCR_015777) | source code, software resource | Source code for the Python implementation of the kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes. | kernel current source density, 1d, 2d, 3d, python, local field potential, transmembrane current source | uses: Python Programming Language | PMID:22091662 | Free, Available for download | SCR_015777 | kernel current source density method - python, kCSD inverse method, Kernel Current Source Density Method | 2026-08-09 09:06:29 | 7 | ||||||||
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lme4 Resource Report Resource Website 100+ mentions |
lme4 (RRID:SCR_015654) | source code, software resource | Software R package. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue." | linear mixed-effects model, s4 class, eigen c++ library, r package, r, bio.tools |
is listed by: CRAN is listed by: bio.tools is listed by: Debian works with: R package: lmerTest |
Free, Available for download | biotools:lme4 | https://cran.r-project.org/package=lme4, https://github.com/lme4/lme4/, https://bio.tools/lme4 | SCR_015654 | lme4, lme4.0, lme4: Linear Mixed-Effects Models using 'Eigen' and S4, lme4: Linear Mixed-Effects Models, R package: lme4 | 2026-08-09 09:06:54 | 411 |
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