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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CMAP Resource Report Resource Website 100+ mentions |
CMAP (RRID:SCR_009034) | CMap | software application, data processing software, software resource, data analysis software | Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, unix, solaris, freebsd, linux, sequence, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite has parent organization: Generic Model Organism Database Project works with: Drug Gene Budger |
PMID:19648141 | GNU General Public License | nlx_153998, OMICS_00933 | https://sourceforge.net/projects/gmod/files/cmap/ | http://www.gmod.org/cmap/, http://gmod.org/wiki/Cmap | SCR_009034 | , GMOD Comparative Mapping (CMap) tool, Comparative Mapping tool, genetic and comparative maps | 2026-02-15 09:19:56 | 413 | ||||
|
SigmaStat Resource Report Resource Website 5000+ mentions |
SigmaStat (RRID:SCR_010285) | SigmaPlot, SigmaStat | organization portal, software application, data visualization software, portal, data processing software, software resource, data or information resource | Software tool for data graphing and analysis by Systat Software, Inc. | is listed by: SoftCite | Commercially available, Free trial available | nlx_157306 | SCR_010285 | SigmaPlot, SigmaStat | 2026-02-15 09:20:21 | 7161 | ||||||||
|
PSIPRED Resource Report Resource Website 1000+ mentions |
PSIPRED (RRID:SCR_010246) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web tool as secondary structure prediction method, incorporating two feed forward neural networks which perform analysis on output obtained from PSI-BLAST. Web server offering analyses of protein sequences. | Predict Secondary Structure, protein analysis, secondary structure prediction, protein sequence, sequence analysis, protein, analysis |
is listed by: Debian is listed by: SoftCite has parent organization: University College London; London; United Kingdom |
Biotechnology and Biological Science Research Council ; University College London |
DOI:10.1093/nar/gkz297 | Free, Freely available | SCR_018546, nlx_156884 | https://sources.debian.org/src/psipred/ | SCR_010246 | PSIPRED Protein Sequence Analysis Workbench, PSIPRED 4.0 | 2026-02-15 09:20:18 | 1688 | |||||
|
TargetScan Resource Report Resource Website 10000+ mentions |
TargetScan (RRID:SCR_010845) | data analysis service, software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals. | predict, biological, target, miRNA, conserved, 8mer, 7mer, site, match seed, region, nonconserved, mismatched, pair |
is listed by: OMICtools is listed by: SoftCite has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
NIGMS GM067031; Howard Hughes Medical Institute ; NSF Graduate Research Fellowship |
PMID:26267216 | Free, Freely available | OMICS_00420 | http://www.targetscan.org/vert_71/ | SCR_010845 | TargetScanFly | 2026-02-15 09:20:25 | 10783 | |||||
|
NIA Array Analysis Resource Report Resource Website 10+ mentions |
NIA Array Analysis (RRID:SCR_010948) | NIA Array Analysis | data analysis service, software resource, data set, service resource, production service resource, data or information resource, analysis service resource | Data analysis server / software designed to test statistical significance of gene microarray data, visualize the results, and provide links to clone information and gene index. Several public datasets are also available. | gene expression, microarray, principal component analysis, significance analysis, gene annotation, anova, hierarchical clustering, pattern matching |
is listed by: OMICtools is listed by: SoftCite has parent organization: National Institute on Aging |
PMID:15734774 | OMICS_00774 | SCR_010948 | 2026-02-15 09:20:25 | 48 | ||||||||
|
FLASH Resource Report Resource Website 1000+ mentions |
FLASH (RRID:SCR_005531) | FLASh | software application, sequence analysis software, data processing software, software resource, data analysis software | 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 |
NLM R01 LM006845; NIGMS R01 GM083873; NHGRI R01 HG006677 |
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 | 2026-02-15 09:18:58 | 2175 | ||||
|
Glimmer Resource Report Resource Website 500+ mentions |
Glimmer (RRID:SCR_011931) | Glimmer | data analysis service, software resource, service resource, production service resource, analysis service 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 | 2026-02-15 09:20:28 | 637 | |||||
|
MAFFT Resource Report Resource Website 10000+ mentions |
MAFFT (RRID:SCR_011811) | MAFFT | software application, data processing software, software resource, alignment software, image analysis software, 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 | 2026-02-15 09:20:24 | 22450 | |||||
|
Mimics Resource Report Resource Website 1000+ mentions |
Mimics (RRID:SCR_012153) | Mimics | software application, image processing software, data processing software, software resource, segmentation software, image analysis software, commercial organization | 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 | 2026-02-15 09:20:27 | 1023 | ||||||||
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SIFT Resource Report Resource Website 10000+ mentions |
SIFT (RRID:SCR_012813) | SIFT | source code, data analysis service, software resource, data access protocol, web service, service resource, production service resource, analysis service resource | 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 | 2026-02-15 09:20:36 | 10223 | |||
|
MACS Resource Report Resource Website 1000+ mentions |
MACS (RRID:SCR_013291) | MACS | software application, data processing software, data analysis software, 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 | 2026-02-15 09:20:42 | 1325 | ||||
|
SABmark Resource Report Resource Website 1+ mentions |
SABmark (RRID:SCR_011817) | SABmark | data or information resource, data set | Downloadable data set designed to assess the performance of both multiple and pairwise (protein) sequence alignment algorithms, and is extremely easy to use. Currently, the database contains 2 sets, each consisting of a number of subsets with related sequences. It''s main features are: * Covers the entire known fold space (SCOP classification), with subsets provided by the ASTRAL compendium * All structures have high quality, with 100% resolved residues * Structure alignments have been derived carefully, using both SOFI and CE, and Relaxed Transitive Alignment * At most 25 sequences in each subset to avoid overrepresentation of large folds* Automated running, archiving and scoring of programs through a few Perl scripts The Twilight Zone set is divided into sequence groups that each represent a SCOP fold. All sequences within a group share a pairwise Blast e-value of at least 1, for a theoretical database size of 100 million residues. Sequence similarity is thus very low, between 0-25% identity, and a (traceable) common evolutionary origin cannot be established between most pairs even though their structures are (distantly) similar. This set therefore represents the worst case scenario for sequence alignment, which unfortunately is also the most frequent one, as most related sequences share less than 25% identity. The Superfamilies set consists of groups that each represent a SCOP superfamily, and therefore contain sequences with a (putative) common evolutionary origin. However, they share at most 50% identity, which is still challenging for any sequence alignment algorithm. Frequently, alignments are performed to establish whether or not sequences are related. To benchmark this, a second version of both the Twilight Zone and the Superfamilies set is provided, in which to each alignment problem a number of false positives, i.e. sequences not related to the original set, are added. Database specifications: * Current version: 1.65 (concurrent with PDB, SCOP and ASTRAL) * Twilight Zone set (with false positives): 209 groups, 1740 (3280) sequences, 10667 (44056) related pairs * Superfamilies set (with false positives): 425 groups, 3280 (6526) sequences, 19092 (79095) related pairs |
is listed by: OMICtools is listed by: SoftCite has parent organization: Vrije Universiteit Brussel; Brussels; Belgium |
PMID:15333456 | OMICS_00988 | SCR_011817 | SABmark - Sequence and structure Alignment Benchmark, Sequence Alignment Benchmark, Sequence and structure Alignment Benchmark | 2026-02-14 02:08:18 | 8 | ||||||||
|
PyMOL Resource Report Resource Website 1000+ mentions |
PyMOL (RRID:SCR_000305) | software application, data visualization software, data processing software, software resource, 3d visualization software | A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures. | visualization, molecule, 3d, molecular structure visualization, molecular visualization system, |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Restricted | nlx_156834, OMICS_03802 | https://sources.debian.org/src/pymol/ | SCR_000305 | 2026-02-15 09:17:54 | 3422 | ||||||||
|
GraphPad Prism Resource Report Resource Website 10000+ mentions Rating or validation data |
GraphPad Prism (RRID:SCR_002798) | software application, data visualization software, data processing software, software resource, data analysis software | Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling. | biostatistics, curve, fitting, nonlinear, regression, graphing, statistical, analysis, biology, pharmacology, physiology |
is listed by: SoftCite has parent organization: GraphPad |
Restricted | rid_000081, SCR_015807 | https://www.graphpad.com/updates/prism-920-release-notes http://graphpad-prism.software.informer.com/5.0/ https://www.graphpad.com/guides/prism/7/user-guide/index.htm |
SCR_002798 | Prism 9.2.0, Graph Pad Prism 7, Graph Pad Prism, GraphPad Prism, Graph pad Prism 5, GraphPad Prism version 9.2.0, Graphpad Prism software, Graph pad Prism 8, Graph pad Prism, Graphpad Prism | 2026-02-15 09:18:23 | 46700 | |||||||
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Clustal W2 Resource Report Resource Website 5000+ mentions |
Clustal W2 (RRID:SCR_002909) | software application, data processing software, software resource, alignment software, service resource, image analysis software | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Command line version of multiple sequence alignment program Clustal for DNA or proteins. Alignment is progressive and considers sequence redundancy. No longer being maintained. Please consider using Clustal Omega instead which accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/ClustalW, GCG/MSF, RSF. | multiple, sequence, alignment, cladogram, phylogram, evolution, phylogenetic, tree, protein, nucleic, acid, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: Clustal Omega is related to: UniProt is related to: Clustal Omega is related to: VectorBase is related to: TopoSNP is related to: Clustal 2 has parent organization: European Bioinformatics Institute has parent organization: University College Dublin; Dublin; Ireland |
Science Foundation Ireland | PMID:17846036 PMID:20439314 DOI:10.1093/bioinformatics/btm404 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02562, nif-0000-30076 | http://www.ch.embnet.org/software/ClustalW.html https://sources.debian.org/src/clustalx/ |
http://www.ebi.ac.uk/tools/clustalw/ | SCR_002909 | European Bioinformatics Institute - ClustalW2 | 2026-02-15 09:18:26 | 7830 | ||||
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SPSS Resource Report Resource Website 10000+ mentions |
SPSS (RRID:SCR_002865) | SPSS | software application, data analytics software, software toolkit, software resource | Software package used for interactive, or batched, statistical analysis in social science, health sciences and marketing. Software platform offers advanced statistical analysis, a library of machine-learning algorithms, text analysis, open-source extensibility, integration with big data and deployment into applications.Versions that were produced by SPSS Inc. before the IBM acquisition (Versions 18 and earlier) would be given origin or publisher of SPSS Inc. in Chicago. | IBM, data, collection, statistics, predict, analyze |
is listed by: SoftCite is related to: IBM SPSS Statistics |
Restricted | SCR_017473, rid_000042 | https://www.ibm.com/products/software | SCR_002865 | Statistical Package for the Social Sciences, IBM SPSS Statistics:International Business Machines SPSS Statistics, IBM SPSS v18, IBM SPSS v17, IBM SPSS v16 | 2026-02-15 09:18:24 | 108532 | ||||||
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Haploview Resource Report Resource Website 5000+ mentions |
Haploview (RRID:SCR_003076) | Haploview | software application, source code, data processing software, software resource | A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site. | linkage disequilibrium, haplotype, genotype, visualization, analysis, single nucleotide polymorphism, gene, genetic, genomic, java |
is listed by: Genetic Analysis Software is listed by: SoftCite is related to: International HapMap Project is related to: PLINK has parent organization: Broad Institute |
PMID:15297300 PMID:21356869 PMID:20147036 |
Free, Available for download, Freely available | nif-0000-30472 | http://www.broad.mit.edu/personal/jcbarret/haploview/ | SCR_003076 | 2026-02-15 09:18:26 | 6933 | ||||||
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NIH Image Resource Report Resource Website 1000+ mentions |
NIH Image (RRID:SCR_003073) | NIH Image | software application, image processing software, data processing software, software resource, source code, image analysis software | Public image processing and analysis program for Macintosh. | image processing application, public image processing software, imagej |
is listed by: SoftCite is related to: ImageJ is related to: BrainImage Software is related to: Object-Image has parent organization: National Institutes of Health has parent organization: National Institute of Mental Health |
NINDS ; NIMH |
Free, download Freely available | nif-0000-30469 | https://imagej.net/nih-image/index.html | SCR_003073 | 2026-02-15 09:18:28 | 4412 | ||||||
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Cytoscape Resource Report Resource Website 10000+ mentions |
Cytoscape (RRID:SCR_003032) | software application, data visualization software, data processing software, software resource, data analysis software | Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. | biological, network, visualization, analysis, data, gene, pathway, molecular, interaction, FASEB list |
is used by: CytoSPADE is used by: HDBase is used by: DisGeNET is used by: categoryCompare lists: PEPPER is listed by: Debian is listed by: SoftCite is related to: PhosphoSitePlus: Protein Modification Site is related to: TRIP Database is related to: CoryneRegNet is related to: AltAnalyze - Alternative Splicing Analysis Tool is related to: MiMI Plugin for Cytoscape is related to: Network Data Exchange (NDEx) is related to: GeneMANIA is related to: DroID - Drosophila Interactions Database is related to: Network-based Prediction of Human Tissue-specific Metabolism is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: DaTo is related to: PiNGO is related to: iBIOFind is related to: cPath is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: ClueGO is related to: RamiGO is related to: EGAN: Exploratory Gene Association Networks has parent organization: Institute for Systems Biology; Washington; USA has parent organization: University of California at San Diego; California; USA is parent organization of: JEPETTO has plug in: CluePedia Cytoscape plugin has plug in: CytoSPADE has plug in: EnrichmentMap has plug in: cytoHubba works with: NetCirChro works with: IMEx - The International Molecular Exchange Consortium works with: yFiles Layout Algorithms works with: RCy3 |
National Resource for Network Biology ; NCRR RR031228; NIGMS GM070743 |
PMID:21149340 PMID:14597658 |
Free, Available for download, Freely available | nif-0000-30404 | https://sources.debian.org/src/cytoscape/ | SCR_003032 | Complex Network Analysis Visualization, Cytoscape 2.6, Cytoscape 3.0 | 2026-02-15 09:18:26 | 23431 | |||||
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BioPerl Resource Report Resource Website 100+ mentions |
BioPerl (RRID:SCR_002989) | BioPerl | source code, software resource, wiki, data or information resource, narrative resource, software repository, software toolkit | BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | perl, biology, ontology, library, sequence, analysis, computational, application, pipeline, bioinformatics, sequence, annotation, module, life science, python, java, genome, software library, parse, manipulate, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: Gene Ontology is related to: OBO has parent organization: Duke University; North Carolina; USA has parent organization: European Bioinformatics Institute is required by: RelocaTE |
NIGMS T32 GM07754-22; NHGRI K22 HG00056; NHGRI K22 HG-00064-01; NHGRI HG00739; NHGRI P41HG02223 |
PMID:12368254 DOI:10.1101/gr.361602 |
Free, Available for download, Freely available | OMICS_04849, nif-0000-30188, biotools:bioperl | https://bio.tools/bioperl https://sources.debian.org/src/bioperl/ |
SCR_002989 | 2026-02-15 09:18:25 | 402 |
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