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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Human Gene Connectome Server Resource Report Resource Website 1+ mentions |
Human Gene Connectome Server (RRID:SCR_002627) | HGCS | service resource, analysis service resource, data analysis service, production service resource | An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways. | gene, disease, phenotype, genome, connectome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Human Gene Connectome |
PMID:23509278 | Free | nlx_156049, biotools:hgcs | https://bio.tools/hgcs | SCR_002627 | 2026-02-15 09:18:21 | 5 | ||||||
|
MLTreeMap Resource Report Resource Website 1+ mentions |
MLTreeMap (RRID:SCR_004792) | MLTreeMap | service resource, analysis service resource, data analysis service, production service resource | Data analysis service that analyzes DNA sequences and determines their most likely phylogenetic origin. Its main use is in metagenomics projects, where DNA is isolated directly from natural environments and sequenced (the organisms from which the DNA originates are often entirely undescribed). It will search such sequences for suitable marker genes, and will use maximum likelihood analysis to place them in the ''''Tree of Life''''. This placement is more reliable than simply assessing the closest relative of a sequence using BLAST. More importantly, MLTreeMap decides not only who is the closest relative of your query sequence, but also how deep in the tree of life it probably branched off. Additionally, MLTreeMap searches the sequences for genes, which are coding for key enzymes of important functional pathways, such as RuBisCo, methane monooxygenase or nitrogenase. In case of a positive hit, MLTreeMap uses maximum likelihood analysis to place them in the respective ''''gene-family tree''''. | phylogeny, gene, fasta, dna sequence, nucleotide sequence, metagenomics, metagenome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: COG has parent organization: University of Zurich; Zurich; Switzerland |
PMID:20687950 | biotools:mltreemap, OMICS_01457 | https://bio.tools/mltreemap | SCR_004792 | Phylogenetic analysis of metagenomics sequence data | 2026-02-15 09:18:54 | 4 | ||||||
|
Ancestrymap Resource Report Resource Website 10+ mentions |
Ancestrymap (RRID:SCR_004353) | ANCESTRYMAP | software application, source code, software resource | Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux. | disease gene, ancestry, gene, genomic, unix, linux, admixture mapping, admixture, genome, linkage disequilibrium, population |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools has parent organization: Harvard Medical School; Massachusetts; USA |
Burroughs Wellcome Fund ; NHGRI K-01 HG002758-01 |
PMID:15088269 | Restricted | nlx_39116, biotools:ancestrymap, OMICS_02083 | https://reich.hms.harvard.edu/software https://bio.tools/ancestrymap |
http://genepath.med.harvard.edu/~reich/Software.htm, http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004353 | 2026-02-15 09:18:45 | 12 | ||||
|
AmphoraNet Resource Report Resource Website 10+ mentions |
AmphoraNet (RRID:SCR_005009) | AmphoraNet | service resource, analysis service resource, data analysis service, production service resource | Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample. | dna sequence, amino acid sequence, dna, sequence, amino acid, phylogenetic, reliability score, nucleotide, protein, nucleotide sequence, protein sequence, phylogenetic analysis, metagenomic, metagenomics, phylotyping, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Eotvos Lorand University; Budapest; Hungary |
PMID:24144838 | Acknowledgement requested, Free, Public | biotools:amphoranet, OMICS_01450 | https://bio.tools/amphoranet | SCR_005009 | 2026-02-15 09:18:53 | 16 | ||||||
|
ProfCom - Profiling of complex functionality Resource Report Resource Website 1+ mentions |
ProfCom - Profiling of complex functionality (RRID:SCR_005797) | ProfCom | service resource, analysis service resource, data analysis service, production service resource | Profiling of Complex Functionality (ProfCom) is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments. A trait which makes ProfCom a unique tool is an ability to profile enrichments of not only available Gene Ontology (GO) terms but also of complex function. A complex function is constructed as Boolean combination of available GO terms. The complex functions inferred by ProfCom are more specific in comparison to single terms and describe more accurately the functional role of genes. Platform: Online tool | gene, function, profile, gene ontology, complex function, statistical analysis, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Institute of Bioinformatics and Systems Biology; Neuherberg; Germany |
DFG | PMID:16959266 | Free for academic use | biotools:profcom, nlx_149276 | https://bio.tools/profcom | SCR_005797 | Profiling of Complex Functionality, Profiling of Complex Functionality (ProfCom) | 2026-02-15 09:19:03 | 4 | ||||
|
SerbGO Resource Report Resource Website |
SerbGO (RRID:SCR_005798) | SerbGO | service resource, analysis service resource, data analysis service, production service resource | SerbGO is a web-based tool intended to assist researchers determine which microarray tools for gene expression analysis which make use of the GO ontologies are best suited to their projects. SerbGO is a bidirectional application. The user can ask for some features by checking on the Query Form to get the appropriate tools for their interests. The user can also compare tools to check which features are implemented in each one. Platform: Online tool | microarray, gene expression, statistical analysis, gene ontology, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Barcelona; Barcelona; Spain |
PMID:18480123 | Free for academic use | nlx_149286, biotools:serbgo | https://bio.tools/serbgo | SCR_005798 | SerbGO - Searching the best GO Tool | 2026-02-15 09:19:12 | 0 | |||||
|
Kismeth Resource Report Resource Website 50+ mentions |
Kismeth (RRID:SCR_005444) | Kismeth | service resource, analysis service resource, data analysis service, production service resource | A web-based tool for bisulfite sequencing analysis that was designed to be used with plants, since it considers potential cytosine methylation in any sequence context (CG, CHG, and CHH). It provides a tool for the design of bisulfite primers as well as several tools for the analysis of the bisulfite sequencing results. Kismeth is not limited to data from plants, as it can be used with data from any species. | plant, methylation, bisulfite sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:18786255 | Free for academic use, Contact for commercial use | biotools:kismeth, OMICS_00602 | https://bio.tools/kismeth | SCR_005444 | 2026-02-15 09:18:58 | 53 | ||||||
|
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit Resource Report Resource Website 10+ mentions |
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit (RRID:SCR_006580) | GOEAST | service resource, analysis service resource, data analysis service, production service resource | Gene Ontology Enrichment Analysis Software Toolkit (GOEAST) is a web based software toolkit providing easy to use, visualizable, comprehensive and unbiased Gene Ontology (GO) analysis for high-throughput experimental results, especially for results from microarray hybridization experiments. The main function of GOEAST is to identify significantly enriched GO terms among give lists of genes using accurate statistical methods. Compared with available GO analysis tools, GOEAST has the following unique features: * GOEAST supports analysis for data from various resources, such as expression data obtained using Affymetrix, illumina, Agilent or customized microarray platforms. GOEAST also supports non-microarray based experimental data. The web-based feature makes GOEAST very user friendly; users only have to provide a list of genes in correct formats. * GOEAST provides visualizable analysis results, by generating graphs exhibiting enriched GO terms as well as their relationships in the whole GO hierarchy. * Note that GOEAST generates separate graph for each of the three GO categories, namely biological process, molecular function and cellular component. * GOEAST allows comparison of results from multiple experiments (see Multi-GOEAST tool). The displayed color of each GO term node in graphs generated by Multi-GOEAST is the combination of different colors used in individual GOEAST analysis. Platform: Online tool | statistical analysis, gene ontology, high-throughput, microarray, hybridization, gene, visualization, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Chinese Academy of Sciences; Beijing; China |
National Natural Science Foundation of China 30725014; National Natural Science Foundation of China 90612019; Ministry of Science and Technology of China 2007CB946901; Chinese Academy of Sciences KSCX2-YW-R-134; Chinese Academy of Sciences KSCX2-YW-N-024 |
PMID:18487275 | Free for academic use | biotools:goeast, nlx_149248 | https://bio.tools/goeast | SCR_006580 | Gene Ontology Enrichment Analysis Software Toolkit, Gene Ontology Enrichment Analysis Software Toolkit (GOEAST) | 2026-02-15 09:19:18 | 38 | ||||
|
GoPubMed Resource Report Resource Website 10+ mentions |
GoPubMed (RRID:SCR_005823) | GoPubMed | data or information resource, database, service resource | A web server which allows users to explore PubMed search results with the Gene Ontology, a hierarchically structured vocabulary for molecular biology. GoPubMed submits a user''''s keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation. Platform: Online tool | other analysis, literature curation and exploration, gene ontology, pubmed, literature, bio.tools |
is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: PubMed has parent organization: Biotechnology Center of the TU Dresden |
European Union IST-2004-506779 | PMID:15980585 | Free for academic use | biotools:gopubmed, nlx_149328, OMICS_01183 | https://bio.tools/gopubmed | SCR_005823 | 2026-02-15 09:19:03 | 29 | |||||
|
Expression Profiler Resource Report Resource Website 1+ mentions |
Expression Profiler (RRID:SCR_005821) | Expression Profiler | service resource, analysis service resource, data analysis service, production service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice. | other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, gene, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Bioinformatics Institute |
European Union ; Wellcome Trust ; Estonian Science Foundation 5724; Estonian Science Foundation 5722 |
PMID:15215431 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:expression_profiler, nlx_149323 | https://bio.tools/expression_profiler | SCR_005821 | Expression Profiler at the EBI | 2026-02-15 09:19:13 | 6 | ||||
|
PIRSF Resource Report Resource Website 10+ mentions |
PIRSF (RRID:SCR_003352) | PIRSF | data or information resource, database, standard specification, narrative resource | A SuperFamily classification system, with rules for functional site and protein name, to facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors. The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains; therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains. There are different PIRSF classification levels. The primary level is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). At a lower level are the subfamilies which are clusters representing functional specialization and/or domain architecture variation within the family. Above the homeomorphic level there may be parent superfamilies that connect distantly related families and orphan proteins based on common domains. Because proteins can belong to more than one domain superfamily, the PIRSF structure is formally a network. The FTP site provides free download for PIRSF. | protein annotation, classification, protein, superfamily, functional site, protein name, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: UniProtKB has parent organization: Protein Information Resource |
NHGRI U01-HG02712; NSF DBI-0138188; NSF ITR-0205470 |
PMID:19455212 PMID:14681371 |
Free, Freely available | biotools:pirsf, nif-0000-03294, OMICS_01697 | https://bio.tools/pirsf | http://pir.georgetown.edu/pirsf/ | SCR_003352 | PIR SuperFamily, Protein Information Resource SuperFamily | 2026-02-15 09:18:32 | 28 | |||
|
Proteomics Identifications (PRIDE) Resource Report Resource Website 500+ mentions |
Proteomics Identifications (PRIDE) (RRID:SCR_003411) | PRIDE | database, service resource, storage service resource, data repository, data or information resource | Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester. | proteomics, protein, peptide, mass spectrometry, annotation, standard, spectra, protein-protein interaction, amino acid, amino acid sequence, post-translational modification, biomart, bio.tools |
is used by: ProteomeXchange is used by: BioSample Database at EBI is recommended by: NIDDK Information Network (dkNET) is listed by: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: HUPO Proteomics Standards Initiative is related to: ProteomeXchange has parent organization: European Bioinformatics Institute |
Wellcome Trust WT085949MA; European Union FP7 LSHG-CT-2006-036814; European Union FP7 260558; European Union FP7 262067; European Union FP7 202272; BBSRC BB/I024204/1 |
PMID:23203882 PMID:19662629 |
Free, Available for download, Freely available | nif-0000-03336, biotools:pride, r3d100011515 | https://www.ebi.ac.uk/pride/archive/ https://bio.tools/pride https://doi.org/10.17616/R3F330 |
SCR_003411 | PRoteomics IDEntifications database, PRIDE Archive - proteomics data repository, PRIDE Archive, PRIDE, Proteomics Identifications, Proteomics Identifications (PRIDE), PRoteomics IDEntifications database (PRIDE) | 2026-02-15 09:18:33 | 642 | ||||
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SplicingCompass Resource Report Resource Website 1+ mentions |
SplicingCompass (RRID:SCR_003249) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software for detection of differential splicing between two different conditions using RNA-Seq data. | differential splicing, splicing event, exon removal, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23449093 | Free, Available for download, Freely available | biotools:splicingcompass, OMICS_01340 | https://github.com/KoenigLabNM/SplicingCompass | SCR_003249 | Splicing Compass | 2026-02-15 09:18:31 | 2 | ||||||
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deFuse Resource Report Resource Website 50+ mentions |
deFuse (RRID:SCR_003279) | software application, sequence analysis software, data processing software, software resource, software toolkit, data analysis software | Software package for gene fusion discovery using RNA-Seq data. It uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. | rna sequencing, gene fusion, paired end alignment, split read, fusion boundary, bio.tools |
uses: SAMTOOLS uses: Bowtie uses: BLAT uses: GMAP uses: R Project for Statistical Computing is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
British Columbia Cancer Foundation ; Vancouver General Hospital Foundation ; Genome Canada ; Michael Smith Foundation for Health Research ; Canadian Breast Cancer Foundation ; Canadian Institutes of Health Research's Bioinformatics Training Program |
PMID:21625565 | Free, Available for download, Freely available | biotools:defuse, OMICS_01345 | https://sourceforge.net/projects/defuse/ http://compbio.bccrc.ca/software/defuse/ https://bio.tools/defuse |
http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page | SCR_003279 | 2026-02-15 09:18:29 | 95 | |||||
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Cell Image Library (CIL) Resource Report Resource Website 10+ mentions |
Cell Image Library (CIL) (RRID:SCR_003510) | CIL | database, service resource, storage service resource, data repository, data or information resource, image repository | Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment. | microscopic image repository, microscopic video repository, cell animation repository, bio.tools |
is used by: NIF Data Federation is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Cell Centered Database is related to: Cell Centered Database is related to: OME-TIFF Format is related to: Integrated Manually Extracted Annotation has parent organization: American Society for Cell Biology has parent organization: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR has parent organization: University of California at San Diego; California; USA is parent organization of: Biological Imaging Methods Ontology |
NIGMS RC2 GM092708 | PMID:34218671 PMID:34218673 |
Free, Freely available | biotools:cellimagelibrary, nif-0000-37639, r3d100011601 | http://www.cellimagelibrary.org/pages/about https://bio.tools/cellimagelibrary https://doi.org/10.17616/R3N92J |
SCR_003510 | Cell Image Library. CIL, Cell Image Library (CIL) | 2026-02-15 09:18:34 | 19 | ||||
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Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | data analysis service, database, service resource, production service resource, data or information resource, analysis service resource | Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
Ontario Research Fund ; European Molecular Biology Laboratory ; NHGRI P41 HG003751; European Union FP6 ENFIN LSHG-CT-2005-518254; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome https://doi.org/10.17616/R3V59P |
SCR_003485 | Reactome Functional Interaction Network | 2026-02-15 09:18:31 | 4282 | |||||
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eTRIKS Resource Report Resource Website 10+ mentions |
eTRIKS (RRID:SCR_003765) | eTRIKS | organization portal, portal, service resource, consortium, data or information resource | Research informatics and analytics platform for the IMI OncoTrack consortium. | data sharing, drug discovery, translational research, informatics, knowledge management, metadata standard, platform, analytics, tool development, bio.tools |
uses: tranSMART is used by: U-BIOPRED is used by: Predict-TB is used by: OncoTrack is used by: ABIRISK is used by: RA MAP is listed by: Consortia-pedia is listed by: Debian is listed by: bio.tools is related to: Roche is related to: Janssen Research and Development is related to: Merck is related to: Pfizer Animal Genetics is related to: Imperial College London; London; United Kingdom is related to: French National Center for Scientific Research is related to: Clinical Data Interchange Standards Consortium is related to: University of Luxembourg; Luxembourg; Luxembourg is related to: IDBS is related to: BioSci Consulting is related to: TraIT is related to: EMIF is related to: Open PHACTS has parent organization: Imperial College London; London; United Kingdom |
Innovative Medicines Initiative ; EFPIA |
PMID:29482119 | biotools:eTRIKS, nlx_158034 | https://bio.tools/eTRIKS | SCR_003765 | European Translational Information and Knowledge Management Services, European Translational Information & Knowledge Management Services | 2026-02-15 09:18:34 | 10 | |||||
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L-Measure Resource Report Resource Website 10+ mentions |
L-Measure (RRID:SCR_003487) | LM | software application, image processing software, data processing software, software resource, service resource, image analysis software | A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux. | neuronal morphology, neuroinformatics, branching analysis, digital reconstruction, analysis, comparison, bio.tools |
is listed by: 3DVC is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: Computational Neuroanatomy Group |
Human Brain Project ; NINDS R01 NS39600 |
PMID:18451794 | Public | nif-0000-00003, biotools:l-measure | http://www.nitrc.org/projects/lmeasure https://bio.tools/l-measure |
SCR_003487 | 2026-02-15 09:18:31 | 30 | |||||
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SeWeR - SEquence analysis using WEb Resources Resource Report Resource Website |
SeWeR - SEquence analysis using WEb Resources (RRID:SCR_004167) | portal, software resource, service resource, data or information resource, topical portal | Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. It doesn''t require any server to host itself. The goal of SeWeR is to turn your web-browser into a powerful sequence-analysis tool. It is written entirely in JavaScript1.2. SeWeR can be downloaded and mirrored freely. The whole package is just around 300K. You can even run it from a floppy. SeWeR is not compatible with Netscape 6. SeWeR now generates graphics. Savvy is a plasmid drawing software that generates plasmid map in the revolutionary Scalable Vector Graphics format from W3C. | nucleic acid, protein, pcr, alignment, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Centre for Cellular and Molecular Biology; Hyderabad; India |
PMID:11395442 | biotools:sewer, nlx_18981 | https://bio.tools/sewer | SCR_004167 | SEquence analysis using WEb Resources, SeWeR | 2026-02-15 09:18:38 | 0 | |||||||
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HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | software application, sequence analysis software, data processing software, software resource, software toolkit, data analysis software | Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning. | analysis, genetic, sequence, multiply, alignment, rate, pattern, data, evolution, platform, python, r, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NSF DBI-0096033; NSF DEB-9996118; NIH R01 AI47745; NIH U01 AI43638; University of California Universitywide AIDS Research Program IS02-SD-701; University of California ; San Diego Center for AIDS Research/NIAID Developmental Award 2 P30 AI36214; NIGMS R01 |
PMID:15509596 | Free, Available for download, Freely available | SCR_016271, biotools:HyPhy, OMICS_04235 | https://sources.debian.org/src/hyphy-pt/ https://veg.github.io/hyphy-site/ https://github.com/veg/hyphy https://bio.tools/HyPhy |
SCR_016162 | HyPhy:Hypothesis Testing using Phylogenies, Hyphy-pt | 2026-02-15 09:21:33 | 1497 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
