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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Philius Resource Report Resource Website |
Philius (RRID:SCR_004625) | Philius | analysis service resource, data analysis service, production service resource, service resource, software resource | Web server that predicts protein transmembrane topology and signal peptides. Hidden Markov models (HMM) have been successfully applied to the tasks of transmembrane protein topology prediction and signal peptide prediction. They expand upon this work by making use of the more powerful class of dynamic Bayesian networks (DBN). Their model, Philius, is inspired by a previously published HMM, Phobius, and combines a signal peptide sub-model with a transmembrane sub-model. They introduce a two-stage DBN decoder which combines the power of posterior decoding with the grammar constraints of Viterbi-style decoding. Philius also provides protein type, segment, and topology confidence metrics to aid in the interpretation of the predictions. | hidden markov model, protein type, segment, topology, confidence metric, prediction, protein, transmembrane, signal peptide, peptide, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:18989393 | nlx_62426, biotools:philius | https://bio.tools/philius | SCR_004625 | 2026-09-12 12:56:15 | 0 | |||||||
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NCBI Structure: Cn3D Resource Report Resource Website 100+ mentions |
NCBI Structure: Cn3D (RRID:SCR_004861) | d visualization software | Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI''s Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features. Cn3D is a tool for visualization of three-dimensional structures with emphasis on interactive examination of sequence-structure relationships and superposition of geometrically similar structures. Can be used to display MMDB structures, superpositions of VAST related structures, and conserved core motifs identified in conserved domains. | gold standard, bio.tools |
is listed by: bio.tools is related to: NCBI Structure has parent organization: NCBI |
PMID:10838572 | biotools:cn3d, nlx_84208 | https://bio.tools/cn3d | SCR_004861 | Cn3D | 2026-09-12 12:56:17 | 133 | |||||||
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MetaPhyler Resource Report Resource Website 10+ mentions |
MetaPhyler (RRID:SCR_004848) | software resource | A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. The classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. The reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database. | metagenome, classification, sequence, taxonomy, genome, microbiome, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: University of Maryland; Maryland; USA |
PMID:21989143 | Acknowledgement requested, Available for download | OMICS_01455, biotools:metaphyler | https://bio.tools/metaphyler | SCR_004848 | MetaPhyler - Estimating Bacterial Composition from Metagenomic Sequences | 2026-09-12 12:56:17 | 11 | ||||||
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hyfi: software suite for binding site search Resource Report Resource Website |
hyfi: software suite for binding site search (RRID:SCR_004884) | software resource | This collection of software is designed to rapidly identify identifies primer and microarray probe binding sites for a query sequence in genomic DNA. This software suite has four main programs:1. A program for indexing a sequence file to speed up the binding site search. 2. A program for retrieving the binding sites of a query sequence. 3. A program for identifying sites where PCR primers could co-operate to exponentially amplify a sequence 4. A program for analyzing a set of binding sites to tailor the search for different reaction conditions. This software is implemented in C. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:16873493 | nlx_85657, biotools:hyfi | https://bio.tools/hyfi | SCR_004884 | Hyfi | 2026-09-12 12:56:18 | 0 | |||||||
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USeq Resource Report Resource Website 100+ mentions |
USeq (RRID:SCR_004753) | USeq | software resource | A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_00499, biotools:useq | https://bio.tools/useq | SCR_004753 | 2026-09-12 12:56:16 | 131 | ||||||||
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NCBI BLAST Resource Report Resource Website 10000+ mentions |
NCBI BLAST (RRID:SCR_004870) | BLAST | data access protocol, data analysis software, data processing software, sequence analysis software, software application, software resource, web service | Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences. | genome, similarity, sequence, nucleotide, protein, gene, data, bio.tools |
is used by: MITE-Tracker is used by: Cello2Go is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: G-BLASTN is related to: genBlastA has parent organization: NCBI is required by: RelocaTE works with: Whole Genome Shotgun (WGS) Project works with: BLASTClust works with: MOLE-BLAST works with: Genotyping |
National Library of Medicine | PMID:16845079 PMID:18440982 |
Free, Freely available, Tutorial available | OMICS_01436, nlx_84530, biotools:blast | http://blast.ncbi.nlm.nih.gov, https://bio.tools/blast, https://sources.debian.org/src/ncbi-blast+/ | SCR_004870 | NCBI Basic Local Alignment Search Tool, NCBI BLAST, Basic Local Alignment Search Tool, BLAST | 2026-09-12 12:56:18 | 17718 | ||||
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miRNAKey Resource Report Resource Website 1+ mentions |
miRNAKey (RRID:SCR_004813) | miRNAKey | software resource | A software pipeline for the analysis of microRNA Deep Sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20801911 | OMICS_00364, biotools:mirnakey | https://bio.tools/mirnakey | SCR_004813 | 2026-09-12 12:56:17 | 6 | |||||||
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SVMerge Resource Report Resource Website 10+ mentions |
SVMerge (RRID:SCR_004777) | SVMerge | software resource | Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available. | structural variant, breakpoint, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:21194472 | biotools:svmerge, OMICS_00325 | https://bio.tools/svmerge | SCR_004777 | SVMerge - Enhanced structural variant and breakpoint detection | 2026-09-12 12:56:16 | 19 | ||||||
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SVseq Resource Report Resource Website 1+ mentions |
SVseq (RRID:SCR_004804) | SVseq | software resource | Software for accurate and efficient calling of structural variations with low-coverage sequence data. Version 2 uses the BAM files of paired Illumina reads with soft-clip signature as input. It calls both deletions and insertions. | structural variant, deletion, insertion, breakpoint, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Connecticut; Connecticut; USA |
PMID:22537045 | OMICS_00327, biotools:svseq | https://bio.tools/svseq | SCR_004804 | SVseq2, SVseq1 | 2026-09-12 12:56:17 | 3 | ||||||
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Minia Resource Report Resource Website 50+ mentions |
Minia (RRID:SCR_004986) | Minia | software resource | A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1748-7188-8-22 | biotools:minia, OMICS_00022 | https://bio.tools/minia, https://sources.debian.org/src/minia/ | SCR_004986 | 2026-09-12 12:56:19 | 66 | |||||||
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SMART Resource Report Resource Website 5000+ mentions |
SMART (RRID:SCR_005026) | SMART | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures. | extracellular, gene, genetic, genetically, genome, architecture, chromatin, domain, mobile, phyletic, protein, proteome, signaling, structure, taxonomic, tertiary, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is listed by: bio.tools is listed by: Debian is related to: Eukaryotic Linear Motif is related to: Conserved Domain Database is related to: GOTaxExplorer has parent organization: EMBL - Bork Group |
European Union | PMID:18978020 PMID:16381859 PMID:14681379 PMID:10592234 PMID:9847187 PMID:9600884 |
Free, Freely available | nif-0000-03471, biotools:smart | http://smart.embl-heidelberg.de/, https://bio.tools/smart | SCR_005026 | Simple Modular Architecture Research Tool | 2026-09-12 12:56:19 | 8432 | ||||
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MIP Scaffolder Resource Report Resource Website 1+ mentions |
MIP Scaffolder (RRID:SCR_005072) | MIP Scaffolder | software resource | A software program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Helsinki; Helsinki; Finland |
OMICS_00044, biotools:mip_scaffolder | https://bio.tools/mip_scaffolder | SCR_005072 | 2026-09-12 12:56:20 | 1 | ||||||||
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959 Nematode Genomes Resource Report Resource Website 1+ mentions |
959 Nematode Genomes (RRID:SCR_006068) | NematodeGenomes | data or information resource, narrative resource, wiki | A collaborative wiki that collates information on completed, ongoing and planned genome and transcriptome sequencing projects on species from phylum Nematoda. The intention is to encourage genome sequencing across the diversity of the phylum Nematoda. Wiki includes: * Published complete nematode genomes: A dynamically generated table of all species for which the genome is published. * Nematode species with genomes in progress: A dynamically generated table of all species for which a genome project is underway. Users may add species to the list * Proposed nematode genome projects: To propose a species for genome sequencing, edit its species page, and set the genome project status to proposed. * BLAST server: Search a number of the nematode-genomes-in-progress with genes of your choice. Currently there are 12 draft genomes available... * Genomes with Data available: Genomes with data available for download. Users may add more data URLs to strain pages or update the URLs. | nematode, genome, genome sequencing, transcriptome sequencing, blast, genomics, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: nematodes.org has parent organization: University of Edinburgh; Scotland; United Kingdom |
NERC | PMID:22058131 | nlx_151473, biotools:959_nematode_genomes | https://bio.tools/959_nematode_genomes | SCR_006068 | NematodeGenomes | 2026-09-12 12:56:35 | 2 | |||||
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MMMDB - Mouse Multiple tissue Metabolome DataBase Resource Report Resource Website 1+ mentions |
MMMDB - Mouse Multiple tissue Metabolome DataBase (RRID:SCR_006064) | MMMDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | MMMDB, Mouse Multiple tissue Metabolome DataBase, is a freely available metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datases are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway. Currently data from cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, and plasma are provided. Non-targeted analyses were performed by capillary electropherograms time-of-flight mass spectrometry (CE-TOFMS) and, therefore, both identified metabolites and unknown (without matched standard) peaks were uploaded to this database. Not only quantified concentration but also processed raw data such as electropherogram, mass spectrometry, and annotation (such as isotope and fragment) are provided. | metabolite, metabolome, cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, plasma, metabolomic pathway, capillary electropherograms time-of-flight mass spectrometry, electropherogram, mass spectrometry, annotation, isotope, fragment, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:22139941 | Free | nlx_151467, biotools:mmmdb | https://bio.tools/mmmdb | SCR_006064 | Mouse Multiple tissue Metabolome DataBase | 2026-09-12 12:56:35 | 1 | |||||
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InterEvol database Resource Report Resource Website 10+ mentions |
InterEvol database (RRID:SCR_006054) | InterEvol | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource | InterEvol database is designed for the analysis of co-evolution events at the interface of known structures of hetero- and homo-oligomers. The database can be search and analyzed through 3 interconnected levels of analysis: * From a Keyword or the PDB entry of a complex, you can browse: ** structural homologs for every chain in other complexes ** structural interologs for every interface ** retrieve pre-computed sequence alignments in diverse species * From 1 or 2 sequences of interacting partners: ** build 2 multiple sequence alignments with the same species ordered in each ** query the InterEvol database with alignments using profile-profile comparison method * Visualize structure vs sequence alignment at the complex interface ** A dedicated Pymol plugin is provided ** Alignment views in Pymol are interactively restricted to the residues selected at the interface | structure, evolution, protein complex, interface, protein complex, sequence alignment, plug in, protein structure, visualization, pymol plugin, structural homolog, structural interolog, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: CEA; Gif sur Yvette; France |
Commissariat a lEnergie Atomique ; ANR HPGenVar |
PMID:22053089 | Free and open to all users - no login requirement | nlx_151453, biotools:interevol | https://bio.tools/interevol | SCR_006054 | 2026-09-12 12:56:34 | 10 | |||||
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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 | 2026-09-12 12:56:35 | 12997 | |||||
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OGEE - Online GEne Essentiality database Resource Report Resource Website 1+ mentions |
OGEE - Online GEne Essentiality database (RRID:SCR_006080) | OGEE, OGEEdb | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Online GEne Essentiality database containing genes that were tested experimentally for essentiality and their features; it also provides a set of tools to systematically explore and analyze these data. The main purpose of this project is to better understand gene essentiality by facilitating the comparisons of the differences and similarities between essential and non-essential genes. This is achieved by collecting not only experimentally tested essential and non-essential genes, but also associated gene features such as expression profiles, duplication status, conservation across species, evolutionary origins and involvement in embryonic development. We focus on large-scale experiments and complement our data with text-mining results. Genes are organized into data sets according to their sources. Genes with variable essentiality status across data sets are tagged as conditionally essential, highlighting the complex interplay between gene functions and environments. Linked tools allow the user to compare gene essentiality among different gene groups, or compare features of essential genes to non-essential genes, and visualize the results. Why is it different from existing databases? * we included both essential and non-essential genes so that we could better understand the gene essentiality by comparing the similarities and differences between the two gene sets; * we compiled a list of features for each gene, including whether they are duplicates or involved in development, the number of other homologous genes in the same genome, as well as their earliest expression stages during development. These features are keys to understand the essentiality of genes; * we also provide a set of tools to explore our data and visualize the results. For example, users can simply divide genes into two groups according to whether they are duplicates, calculate the proportion of essential genes (PE%) in each group and then visualize the results in a bar plot; or they can classify genes into multiple groups according to their earliest expression stages during evolution, compare the essentiality of genes that were expressed earlier with those were latter, and plot the results in a line chart. | genome-wide association study, essentiality, gene, essential gene, non-essential gene, growth, expression profile, duplication status, conservation, evolutionary origin, embryonic development, text-mining, gene function, environment, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
BMBF 0315450C | PMID:22075992 | Free | nlx_151488, biotools:ogee | https://bio.tools/ogee | SCR_006080 | Online GEne Essentiality database | 2026-09-12 12:56:35 | 2 | ||||
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ICEberg Resource Report Resource Website 50+ mentions |
ICEberg (RRID:SCR_006026) | ICEberg | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | ICEberg is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. ICEberg will facilitate efficient, multidisciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community. | dna, protein, sequence, chromosome, element, gene, similarity search, sequence alignment, genome, phylogenetic, functional analysis, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Shanghai Jiao Tong University; Shanghai; China |
National Natural Science Foundation of China 973 program 2009CB118901; National Natural Science Foundation of China 973 program 2012CB721002; National Natural Science Foundation of China 863 program 2011BAD23B05-3; Ministry of Science and Technology China ; Ministry of Education China NCET-10-0572; Shanghai Jiaotong University ; Shanghai Municipality ; Action Medical Research SP4255; Innovation Fellowship ; East Midlands Development Agency |
PMID:22009673 | nlx_151424, biotools:iceberg | https://bio.tools/iceberg | SCR_006026 | ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria | 2026-09-12 12:56:34 | 89 | |||||
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h5vc Resource Report Resource Website 1+ mentions |
h5vc (RRID:SCR_006039) | h5vc | software resource | Software package that contains functions to interact with tally data from Next-Generation Sequencing (NGS) experiments that is stored in HDF5 files. | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Bioinformatics Institute |
PMID:24451629 | GNU General Public License, v3 or newer | biotools:h5vc, OMICS_02243 | http://www.ebi.ac.uk/~pyl/h5vc/, https://bio.tools/h5vc | SCR_006039 | h5vc - Scalable nucleotide tallies with HDF5, h5vc - Managing alignment tallies using a hdf5 backend | 2026-09-12 12:56:34 | 2 | |||||
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Polbase Resource Report Resource Website |
Polbase (RRID:SCR_006107) | data or information resource, data repository, database, service resource, storage service resource | Repository of biochemical, genetic, and structural information about DNA Polymerases. Polbase is designed to compile detailed results of polymerase experimentation, presenting them in a dynamic view to inform further research. After validation, results from references are displayed in context with relevant experimental details and are always traceable to their source publication. Polbase is connected to other resources, including PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase knowledge. In addition to a simple web interface, Polbase data is exposed for custom analysis by external software. | dna polymerase repository, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: PubMed is related to: UniProt has parent organization: New England Biolabs |
Small Business Innovation Research ; NIGMS 1R44GM087021 |
PMID:21993301 | Free, Open unspecified license, Acknowledgement required | biotools:polbase, nlx_151580 | https://bio.tools/polbase | SCR_006107 | DNA Polymerase Database | 2026-09-12 12:56:35 | 0 |
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