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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FLASH Resource Report Resource Website 1000+ mentions |
FLASH (RRID:SCR_005531) | FLASh | data analysis software, data processing software, sequence analysis software, software application, software resource | Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: shovill is related to: CLIP-Explorer has parent organization: Johns Hopkins University; Maryland; USA |
NHGRI R01 HG006677; NIGMS R01 GM083873; NLM R01 LM006845 |
PMID:21903629 | Free, Available for download, Freely available | biotools:flash, OMICS_01047 | https://sourceforge.net/projects/flashpage/files/, https://bio.tools/flash, https://sources.debian.org/src/flash/ | SCR_005531 | Fast Length Adjustment of SHort reads, Fast Length Adjustment of Short reads | 2026-09-19 12:50:55 | 2461 | ||||
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RAxML Resource Report Resource Website 10000+ mentions |
RAxML (RRID:SCR_006086) | RAxML | data analysis software, data processing software, software application, software resource | Software program for phylogenetic analyses of large datasets under maximum likelihood. | phylogeny, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: RAxML Next Generation works with: PAML |
PMID:24451623 PMID:16928733 PMID:15608047 DOI:10.1093/bioinformatics/btu033 |
GNU General Public License | biotools:raxml, OMICS_02242 | https://bio.tools/raxml, https://sources.debian.org/src/raxml/ | SCR_006086 | Randomized Axelerated Maximum Likelihood | 2026-09-19 12:51:04 | 12997 | |||||
|
microRNA.org Resource Report Resource Website 1000+ mentions |
microRNA.org (RRID:SCR_006997) | microRNA.org | data or information resource, database, software resource | Database of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. MicroRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. This website enables users to explore: * The set of genes that are potentially regulated by a particular microRNA. * The implied cooperativity of multiple microRNAs on a particular mRNA. * MicroRNA expression profiles in various mammalian tissues. The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation. The microRNA Target Detection Software, miRanda, is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microrna, gene, expression, gene regulation, FASEB list |
is listed by: OMICtools is listed by: SoftCite |
NIGMS ; Atlantic Philanthropies ; Alfred W. Bressler Scholars Endowment Fund |
PMID:18158296 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03127, OMICS_00402 | SCR_006997 | microRNA.org - Targets and Expression | 2026-09-19 12:51:22 | 2818 | |||||
|
WFU PickAtlas Resource Report Resource Website 1000+ mentions |
WFU PickAtlas (RRID:SCR_007378) | PickAtlas | data processing software, image processing software, software application, software resource | A software toolbox that provides a method for generating Region of Interest (ROI) masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label (gyral anatomy), and Tissue type. The atlases have been extended to the vertex in MNI space, and corrected for the precentral gyrus anomaly. Additional atlases (including non-human atlases) can be added without difficulty., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | neuroanatomy, cytoarchitecture, fmri, matlab, brain, brain region, talairach daemon, analyze, atlas application, matlab, microsoft, magnetic resonance, posix/unix-like, win32 (ms windows), windows, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: SoftCite is related to: Talairach Daemon has parent organization: Wake Forest School of Medicine; North Carolina; USA |
NIBIB 1R03EB008670 | PMID:12880848 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00358 | SCR_007378 | WFU_PickAtlas | 2026-09-19 12:51:28 | 1276 | |||||
|
CCP4 Resource Report Resource Website 1000+ mentions |
CCP4 (RRID:SCR_007255) | CCP4 | data analysis software, data or information resource, data processing software, portal, service resource, simulation software, software application, software resource | Portal for Macromolecular X-Ray Crystallography to produce and support an integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques. Used in the education and training of scientists in experimental structural biology for determination and analysis of protein structure. | macromolecular, x-ray, crystallography, biophysical, technique, structural, biology, analysis, protein, Research Complex at Harwell, computational, collaborative, project |
is used by: MoRDa is used by: PDB-REDO is listed by: SoftCite is related to: BALBES is related to: CCP4mg is related to: fragon is related to: ConPlot has parent organization: Science and Technology Facilities Council |
Science and Technology Facilities Council | Free, Available for download, Freely available, Tutorial available | SCR_016709, nif-0000-30238 | SCR_007255 | The Collaborative Computational Project Number 4 in Protein Crystallography, Collaborative Computational Project Number 4 | 2026-09-19 12:51:26 | 4896 | ||||||
|
Imaris Resource Report Resource Website 10000+ mentions |
Imaris (RRID:SCR_007370) | data processing software, image analysis software, software application, software resource | Imaris provides range of capabilities for working with three dimensional images. Uses flexible editing and processing functions, such as interactive surface rendering and object slicing capabilities. And output to standard TIFF, Quicktime and AVI formats. Imaris accepts virtually all image formats that are used in confocal microscopy and many of those used in wide-field image acquisition. Imaris version 10.1 for image analysis workflows using AI trainable object detection. | Three dimensional images, 3D image, AI trainable object detection, |
is used by: Simple Assignment of Spots to Surfaces is listed by: SoftCite is related to: FilamentTracer is related to: ImarisViewer |
Restricted | nif-0000-00314 | https://imaris.oxinst.com/, https://imaris.oxinst.com/newrelease | SCR_007370 | , Imaris 10.1, Imaris 9.7 | 2026-09-19 12:51:28 | 16914 | |||||||
|
BioEdit Resource Report Resource Website 10000+ mentions |
BioEdit (RRID:SCR_007361) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software tool as biological sequence alignment editor written for Windows 95/98/NT/2000/XP/7 and sequence analysis program. Provides sequence manipulation and analysis options and links to external analysis programs to view and manipulate sequences with simple point and click operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, alignment, editor, analysis, program | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156845 | SCR_007361 | 2026-09-19 12:51:28 | 13403 | |||||||||
|
RMS Resource Report Resource Website 1+ mentions |
RMS (RRID:SCR_007415) | RMS | data or information resource, job resource, portal, topical portal, training resource | It is at the forefront of new ideas and developments in microscopy and imaging. The RMS is the only truly international microscopical society, drawing distinguished members from all over the world. It also serves the needs of its company members who represent all the major manufacturers and suppliers of microscopes, equipment and services. In addition to this, the Society is pursuing an initiative to encourage young microscope users who may go on to influence microscopy in years to come. The Society is dedicated to advancing science, developing careers and supporting wider understanding of science and microscopy through its Science and Society activities. In support of the above, it publishes The Journal of Microscopy and microscopy handbooks, as well as helping young scientists through bursaries. The Society is incorporated by Royal Charter. Its governing documents are its Charter and By-laws. The most recent AGM minutes, Trustees Report and Accounts are available below - 2007 AGM draft minutes Full 2007 Trustees Report and Accounts - as submitted to the Charity Commission The RMS is a member of: - the Foundation for Science and Technology - the Biosciences Federation - the International Federation of Societies for Microscopy - the European Microscopy Society training opportunities; jobs. | is listed by: SoftCite | nif-0000-00498 | SCR_007415 | The Royal Microscopical Society | 2026-09-19 12:51:29 | 6 | |||||||||
|
MAFFT Resource Report Resource Website 10000+ mentions |
MAFFT (RRID:SCR_011811) | MAFFT | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments. | alignment, amino acid, nucleotide, sequence, DNA, sequence alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
EMBL ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:12136088 PMID:17118958 PMID:16362903 PMID:15661851 PMID:18439255 PMID:23023983 DOI:10.1093/bib/bbn013 |
biotools:MAFFT, OMICS_00979 | https://www.ebi.ac.uk/Tools/msa/mafft/, https://www.genome.jp/tools-bin/mafft, https://myhits.isb-sib.ch/cgi-bin/mafft, https://bio.tools/MAFFT, https://sources.debian.org/src/mafft/ | SCR_011811 | Multiple Alignment using Fast Fourier Transform, MAFFT version 5, MAFFT version 7 | 2026-09-19 12:52:18 | 24687 | |||||
|
CGView Resource Report Resource Website 100+ mentions |
CGView (RRID:SCR_011779) | CGView | software resource | A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Alberta; Alberta; Canada |
DOI:10.1093/bioinformatics/bti054 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00905, biotools:cgview | https://bio.tools/cgview, https://sources.debian.org/src/cgview/ | SCR_011779 | Circular Genome Viewer | 2026-09-19 12:52:18 | 310 | |||||
|
Infernal Resource Report Resource Website 500+ mentions |
Infernal (RRID:SCR_011809) | Infernal | software resource | Software for searching DNA sequence databases for RNA structure and sequence similarities. | FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: ANNOgesic has parent organization: Janelia Research |
PMID:24008419 DOI:10.1093/bioinformatics/btp157 |
GNU General Public License, v3 | OMICS_00977 | https://sources.debian.org/src/infernal/ | SCR_011809 | Infernal: inference of RNA alignments, INFERence of RNA Alignment | 2026-09-19 12:52:18 | 772 | |||||
|
Glimmer Resource Report Resource Website 500+ mentions |
Glimmer (RRID:SCR_011931) | Glimmer | analysis service resource, data analysis service, production service resource, service resource, software resource | A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. | microbial, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Glimmer-MG is related to: GlimmerHMM has parent organization: Johns Hopkins University; Maryland; USA |
DOI:10.1093/nar/26.2.544 | Open unspecified license, OSI certified | OMICS_01486, biotools:glimmer | https://bio.tools/glimmer, https://sources.debian.org/src/tigr-glimmer/ | SCR_011931 | Glimmer - Microbial Gene-Finding System | 2026-09-19 12:52:21 | 687 | |||||
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AutoDock Vina Resource Report Resource Website 1000+ mentions |
AutoDock Vina (RRID:SCR_011958) | AutoDock Vina | software resource | An open-source program for doing molecular docking. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Scripps Research Institute |
PMID:34278794 PMID:19499576 DOI:10.1002/jcc.21334 |
Open unspecified license | biotools:autodock_vina, OMICS_01595, OMICS_03790 | https://bio.tools/autodock_vina, https://sources.debian.org/src/avogadro/ | SCR_011958 | 2026-09-19 12:52:21 | 2447 | ||||||
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MrBayes Resource Report Resource Website 10000+ mentions |
MrBayes (RRID:SCR_012067) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. | applet, mac os x, unix/linux, windows |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:22357727 DOI:10.1093/sysbio/sys029 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04237 | https://sources.debian.org/src/mrbayes/ | SCR_012067 | 2026-09-19 12:52:24 | 10714 | |||||||
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Mimics Resource Report Resource Website 1000+ mentions |
Mimics (RRID:SCR_012153) | Mimics | commercial organization, data processing software, image analysis software, image processing software, segmentation software, software application, software resource | Software for medical image processing. Use Mimics for the segmentation of 3D medical images (coming from CT, MRI, microCT, CBCT, Ultrasound, Confocal Microscopy) and the result will be highly accurate 3D models of your patient''s anatomy. You can then use these patient-specific models for a variety of engineering applications directly in Mimics or 3-matic, or export the 3D models and anatomical landmark points to 3rd party software, like statistical, CAD, or FEA packages. | segmentation, 3d-rendering, micro-ct, ct, mri, cbct, ultrasound, confocal microscopy, anatomy | is listed by: SoftCite | rid_000086 | SCR_012153 | Materialise MIMICS, Mimics - Medical Image Segmentation for Engineering on Anatomy | 2026-09-19 12:52:26 | 1029 | ||||||||
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SIFT Resource Report Resource Website 10000+ mentions |
SIFT (RRID:SCR_012813) | SIFT | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, source code, web service | Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available. | gene, genetic, genomic, amino acid, substitution, protein function, coding region, single nucleotide variant, coding indel, deletion, insertion, sequence, protein, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SIFT 4G has parent organization: Genome Institute of Singapore; Singapore; Singapore has parent organization: J. Craig Venter Institute |
Agency for Science Technology and Research ; NIGMS GM29009 |
PMID:19561590 PMID:12824425 PMID:11337480 DOI:10.1038/nprot.2009.86 |
Non-commercial | biotools:sift, OMICS_00137, nlx_154618 | http://sift.jcvi.org/, https://bio.tools/sift, https://sources.debian.org/src/sift/ | http://sift.bii.a-star.edu.sg/SIFT.html | SCR_012813 | Sorting Intolerant From Tolerant | 2026-09-19 12:52:33 | 10996 | |||
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lumi Resource Report Resource Website 100+ mentions |
lumi (RRID:SCR_012781) | lumi | software resource | Software that provides an integrated solution for the Illumina microarray data analysis. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
biotools:lumi, OMICS_00770 | https://bio.tools/lumi | SCR_012781 | 2026-09-19 12:52:32 | 319 | ||||||||
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Ringo Resource Report Resource Website 10+ mentions |
Ringo (RRID:SCR_012973) | Ringo | software resource | Software package that facilitates the primary analysis of ChIP-chip data. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
OMICS_00809 | SCR_012973 | 2026-09-19 12:52:36 | 38 | ||||||||||
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MACS Resource Report Resource Website 1000+ mentions |
MACS (RRID:SCR_013291) | MACS | data analysis software, data processing software, software application, software resource | Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity. | identify, transcript, factor, binding, site, model, based, analysis, CHIP Seq, short, read, sequencer, protein, DNA, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Dana-Farber Cancer Institute |
NHGRI HG004069; NHGRI HG004270; NIDDK DK074967 |
PMID:18798982 DOI:10.1186/gb-2008-9-9-r137 |
Free, Available for download, Freely available | OMICS_00446, biotools:macs | https://bio.tools/macs, https://sources.debian.org/src/macs/ | SCR_013291 | MACS - Model-based Analysis for ChIP-Seq, Model-based Analysis for ChIP-Seq, MACS2 | 2026-09-19 12:52:40 | 1418 | ||||
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BioMoby Resource Report Resource Website 1+ mentions |
BioMoby (RRID:SCR_013386) | controlled vocabulary, data or information resource, ontology | The MOBY-S system defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next. The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. Sponsors: Funding was provided by Genome Prairie and Genome Alberta A Bioinformatics Platform for Genome Canada''; Canadian Institutes for Health Research; The Natural Sciences and Engineering Research Council of Canada; The Heart and Stroke Foundation for BC and Yukon; The EPSRC through the myGrid (GR/R67743/01, EP/C536444/1, EP/D044324/1, GR/T17457/01) e-Science projects; The Spanish National Institute for Bioinformatics (INB) through Fundacin Genoma Espaa; The Generation Challenge Programme (GCP; http://www.generationcp.org) of the Consultative Group for International Agricultural Research. :Keywords: Ontology, Messaging, Standard, Client, Automatically, Discovery, Biological, Data, ANalytical, Service, Model, Organism, Database, Java, Platform, Semantic, Bioinformatics, |
is listed by: SoftCite is related to: BioExtract has parent organization: Pompeu Fabra University; Barcelona; Spain |
nif-0000-30186 | SCR_013386 | BioMoby | 2026-09-19 12:52:42 | 8 |
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