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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GreenPhylDB Resource Report Resource Website 10+ mentions |
GreenPhylDB (RRID:SCR_002834) | GreenPhylDB | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs. | comparative genomics, genome, functional genomics, genomics, gene family, homolog, bio.tools |
uses: Gene Ontology is listed by: bio.tools is listed by: Debian has parent organization: CIRAD |
PMID:20864446 | Free, Freely available, Available for download | biotools:greenphyldb, nif-0000-02928 | http://greenphyl.cirad.fr http://www.greenphyl.org/v3/ https://bio.tools/greenphyldb |
SCR_002834 | 2026-02-16 09:46:01 | 19 | ||||||
|
Primer3Plus Resource Report Resource Website 1000+ mentions |
Primer3Plus (RRID:SCR_003081) | Primer3Plus | data analysis service, analysis service resource, software resource, source code, production service resource, service resource | A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. | primer, dna sequence, primer design, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Primer3 has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
Howard Hughes Medical Institute ; NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:17485472 | Free, Freely available | biotools:primer3plus, OMICS_02347 | https://bio.tools/primer3plus | SCR_003081 | Primer3Plus - pick primers from a DNA sequence | 2026-02-16 09:45:55 | 1673 | ||||
|
FSL Resource Report Resource Website 1000+ mentions |
FSL (RRID:SCR_002823) | software resource, software toolkit, software library | Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas. | dti, brain, imaging, data, structural, mri, diffusion, function, preprocessing, analysis, statistical, tractography, atlas, neuroimaging, parameter, reconstruction, volumetric, segmentation, independent, component, temporal, transformation |
uses: Neuroimaging Data Model is used by: Spinal Cord Toolbox is used by: Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND) is used by: XFSL: An FSL toolbox is used by: CMIND PY lists: SUSAN lists: FUGUE lists: Miscvis lists: BayCEST lists: ICA-PNM is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: Rodent Brain Extraction Tool is related to: Human Connectome Coordination Facility is related to: BASH4RfMRI is related to: DW-MRI registration in FSL is related to: FSL extensions is related to: Diffusion MRI of Traumatic Brain Injury is related to: Segmentation of Hippocampus Subfields is related to: masked ICA (mICA) Toolbox has parent organization: University of Oxford; Oxford; United Kingdom has plug in: Multivariate Exploratory Linear Optimized Decomposition into Independent Components has plug in: FMRI Expert Analysis Tool has plug in: FABBER has plug in: BASIL has plug in: VERBENA has plug in: Brain Extraction Tool has plug in: FMRIB's Automated Segmentation Tool has plug in: FMRIB’s Integrated Registration and Segmentation Tool has plug in: Harvard - Oxford Cortical Structural Atlas has plug in: FMRIB's Linear Image Registration Tool has plug in: FNIRT has plug in: FSLVBM has plug in: SIENA has plug in: SIENAX has plug in: Multimodal Image Segmentation Tool has plug in: Brain Intensity AbNormality Classification Algorithm has plug in: Multimodal Surface Matching has plug in: fsl_anat has plug in: FMRIB's Diffusion Toolbox has plug in: Tract Based Spatial Statistics has plug in: XTRACT has plug in: eddy has plug in: topup has plug in: eddyqc has plug in: randomise has plug in: PALM has plug in: fsl-cluster has plug in: FDR has plug in: DualRegression has plug in: FLOBS has plug in: FSLeyes has plug in: Fslutils has plug in: Atlasquery has plug in: MCFLIRT has plug in: POSSUM has plug in: FSL-MRS |
EPSRC ; MRC ; BBSRC ; GlaxoSmithKline ; Pfizer |
PMID:21979382 PMID:19059349 PMID:15501092 |
Free, Available for download, Freely available | nif-0000-00305, birnlex_2067, SCR_007368 | http://www.nitrc.org/projects/fsl http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ https://sources.debian.org/src/fsl/ |
SCR_002823 | , FMRIB Software Library, fMRIB Software Library, Functional Magnetic Resonance Imaging of the Brain Software Library | 2026-02-16 09:46:01 | 4685 | |||||
|
DIALIGN Resource Report Resource Website 10+ mentions |
DIALIGN (RRID:SCR_003041) | DIALIGN | web service, data analysis service, analysis service resource, data access protocol, software resource, production service resource, service resource | Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/ | dna, protein, sequence alignment, sequence, alignment, fasta, genome, genomic sequence, homology, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15215344 PMID:23620293 DOI:10.1186/1748-7188-3-6 |
Free, Available for download, Freely available | nif-0000-30417, OMICS_24606, OMICS_00973, biotools:dialign-tx | http://dialign.gobics.de/ https://bio.tools/dialign-tx |
https://sources.debian.org/src/dialign-tx/ | SCR_003041 | DIALIGN at GOBICS | 2026-02-16 09:46:06 | 43 | ||||
|
CTDopts Resource Report Resource Website |
CTDopts (RRID:SCR_023997) | source code, software resource | Software gives your command-line tools a CTD-compatible interface. Module for enabling tools with CTD reading/writing, argument parsing, validating and manipulating capabilities. | command-line tools, CTD-compatible interface, module for enabling tools, CTD reading/writing, argument parsing, validating and manipulating capabilities, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ctdopts/ | SCR_023997 | ctdopts | 2026-02-15 09:23:17 | 0 | ||||||||
|
Htscodecs Resource Report Resource Website |
Htscodecs (RRID:SCR_024034) | source code, software resource | Software repository implements the custom CRAM codecs used for "EXTERNAL" block types.Custom compression for CRAM custom algorithm written to compress the BAM file format for DNA sequencing data. | custom CRAM codecs, EXTERNAL" block types, custom compression for CRAM, compress the BAM file format, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/htscodecs/ | SCR_024034 | htscodecs | 2026-02-15 09:23:18 | 0 | ||||||||
|
conda-package-handling Resource Report Resource Website |
conda-package-handling (RRID:SCR_023991) | source code, software resource | Software to create and extract conda packages of various formats. | Create and extract conda packages, various formats, conda packages, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/conda-package-handling/ https://conda.github.io/conda-package-handling/ |
SCR_023991 | 2026-02-15 09:23:30 | 0 | |||||||||
|
ELPH Resource Report Resource Website |
ELPH (RRID:SCR_024011) | source code, software resource | Software tool as general purpose Gibbs sampler for finding motifs in set of DNA or protein sequences.Takes as input a set containing sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. Used to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs). | Gibbs sampler, finding motifs, DNA sequences, protein sequences, common motif search, find patterns, ribosome binding sites, exon splicing enhancers, | is listed by: Debian | Free, Available for download, Freely available | OMICS_24617 | https://sources.debian.org/src/elph/ | SCR_024011 | Estimated Locations of Pattern Hits, elph | 2026-02-15 09:22:34 | 0 | |||||||
|
CCS Resource Report Resource Website 10+ mentions |
CCS (RRID:SCR_024379) | source code, software resource | Software to generate highly accurate single molecule consensus reads. | HiFi Reads, generate highly accurate single molecule consensus reads, generate consensus reads, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_26281 | https://sources.debian.org/src/unanimity/ | SCR_024379 | ccs ; unanimity | 2026-02-15 09:23:28 | 23 | |||||||
|
alleleCount Resource Report Resource Website 10+ mentions |
alleleCount (RRID:SCR_023961) | source code, software resource | Software package to prevent code duplication. Support code for NGS copy number algorithms. Generates count of coverage of each allele ACGT at that location given any filter settings. | NGS copy number, allele ACGT coverage, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/allelecount/ http://cancerit.github.io/alleleCount/ |
SCR_023961 | allelecount | 2026-02-15 09:23:29 | 12 | ||||||||
|
Fast5 Library Resource Report Resource Website |
Fast5 Library (RRID:SCR_024023) | source code, software resource | Software C++ library for accessing Oxford Nanopore Technologies sequencing data. | C++ library, accessing Oxford Nanopore Technologies sequencing data, | is listed by: Debian | Free, Available for download, Freely available | OMICS_29589 | https://sources.debian.org/src/fast5/ | SCR_024023 | Fast5, fast5 | 2026-02-15 09:23:20 | 0 | |||||||
|
python-biom-format Resource Report Resource Website 1+ mentions |
python-biom-format (RRID:SCR_024193) | source code, software resource | Software provides command line interface and Python API for working with Biological Observation Matrix files. | command line interface, Python API for working with Biological Observation Matrix files, BIOM files, |
is listed by: Debian is related to: biomformat |
PMID:23587224 | Free, Available for download, Freely available, | https://sources.debian.org/src/python3-biom-format/ | SCR_024193 | 2026-02-15 09:23:36 | 1 | ||||||||
|
BAIT Resource Report Resource Website 1+ mentions |
BAIT (RRID:SCR_000511) | BAIT | software application, data processing software, data visualization software, data analysis software, software resource | Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. | create strand inheritance plots, strand-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24028793 | Free, Available for download, Freely available | biotools:bait, OMICS_01531 | https://bio.tools/bait | SCR_000511 | BAIT - Software to help analyse Strand-Seq data | 2026-02-16 09:45:16 | 1 | |||||
|
MPscan Resource Report Resource Website |
MPscan (RRID:SCR_000587) | MPscan | data access protocol, software resource, web service | Web tool for index free mapping of multiple short reads on a genome. | linux, macos, next-generation sequencing, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: ATGC: Montpellier bioinformatics platform |
Free, Available for download, Freely available | biotools:mpscan, OMICS_00670 | https://bio.tools/mpscan | SCR_000587 | MPscan: index free mapping of multiple short reads on a genome | 2026-02-16 09:45:17 | 0 | ||||||
|
Skylign Resource Report Resource Website 10+ mentions |
Skylign (RRID:SCR_001176) | Skylign | data analysis service, analysis service resource, software resource, production service resource, service resource | A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. | sequence alignment, profile, logo, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Janelia Research |
PMID:24410852 | Creative Commons Attribution License, v3 Unported | biotools:skylign, OMICS_02182 | https://bio.tools/skylign | SCR_001176 | Skylign - Interactive logos for alignments and profile HMMs | 2026-02-16 09:45:25 | 13 | |||||
|
sim4cc Resource Report Resource Website |
sim4cc (RRID:SCR_001204) | software application, data processing software, image analysis software, software resource, alignment software | Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species. | Cross species spliced alignment, unix, sequence alignment, cdna sequence, genomic sequence, homolog, gene, splice, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johns Hopkins University; Maryland; USA |
NSF CLS20163A; Sloan Research Fellowship ; NLM R01 LM006845 |
PMID:19429899 | Free, Available for download, Freely available | biotools:sim4cc, OMICS_02145 | https://bio.tools/sim4cc | SCR_001204 | 2026-02-16 09:45:26 | 0 | ||||||
|
bsseq Resource Report Resource Website 1+ mentions |
bsseq (RRID:SCR_001072) | software application, data processing software, sequence analysis software, data analysis software, software resource | R package with tools for analyzing and visualizing bisulfite sequencing data. | bisulfite sequencing, analyze, r, sequence analysis software, data analysis software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01847, biotools:bsseq | https://bio.tools/bsseq | SCR_001072 | bsseq - Analyze manage and store bisulfite sequencing data | 2026-02-16 09:45:24 | 8 | |||||||
|
SplitSeek Resource Report Resource Website 1+ mentions |
SplitSeek (RRID:SCR_001012) | software application, data processing software, sequence analysis software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data. | bioinformatics alignment, sequence analysis software, de novo, prediction, rna seq, rna, splice junction, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20236510 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:splitseek, OMICS_01253 | https://bio.tools/splitseek | http://www.uppmax.uu.se/software/splitseek | SCR_001012 | 2026-02-16 09:45:23 | 1 | ||||||
|
AutoAssemblyD Resource Report Resource Website |
AutoAssemblyD (RRID:SCR_001087) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers. | genome, genome assembly, xml, sequence analysis software, local genome assembly, remote genome assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24143057 | Free, Available for download, Freely available | biotools:autoassemblyd, OMICS_00874 | https://bio.tools/autoassemblyd | SCR_001087 | 2026-02-16 09:45:25 | 0 | |||||||
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Happy Resource Report Resource Website 10+ mentions |
Happy (RRID:SCR_001395) | HAPPY | software application, data processing software, data analysis software, source code, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download). | qtl, quantitative trait locus, r, c, gene, genetic, genomic, ansi c, unix, irix, sunos, linux, animal model, trait, map, genotype, phenotype, haplotype, linear regression, data set, qtl mapping |
is listed by: Genetic Analysis Software is listed by: Debian has parent organization: Wellcome Trust Centre for Human Genetics |
Wellcome Trust | PMID:11050180 DOI:10.1073/pnas.230304397 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152594 | http://www.well.ox.ac.uk/~rmott/happy.html | https://sources.debian.org/src/r-other-mott-happy.hbrem/ | SCR_001395 | reconstructing HAPlotYpes | 2026-02-16 09:45:28 | 46 |
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