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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MLTreeMap Resource Report Resource Website 1+ mentions |
MLTreeMap (RRID:SCR_004792) | MLTreeMap | service resource, production service resource, analysis service resource, data analysis service | 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 | 2026-07-30 09:27:02 | 4 | ||||||
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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, production service resource, analysis service resource, data analysis service | 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) | 2026-07-30 09:27:26 | 38 | ||||
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ProfCom - Profiling of complex functionality Resource Report Resource Website 1+ mentions |
ProfCom - Profiling of complex functionality (RRID:SCR_005797) | ProfCom | service resource, production service resource, analysis service resource, data analysis service | 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) | 2026-07-30 09:27:14 | 4 | ||||
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SerbGO Resource Report Resource Website |
SerbGO (RRID:SCR_005798) | SerbGO | service resource, production service resource, analysis service resource, data analysis service | 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 | 2026-07-30 09:27:15 | 0 | |||||
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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 | 2026-07-30 09:27:15 | 29 | |||||
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Expression Profiler Resource Report Resource Website 1+ mentions |
Expression Profiler (RRID:SCR_005821) | Expression Profiler | service resource, production service resource, analysis service resource, data analysis service | 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 | 2026-07-30 09:27:14 | 6 | ||||
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PRED-TMBB Resource Report Resource Website 50+ mentions |
PRED-TMBB (RRID:SCR_006190) | PRED-TMBB | service resource, production service resource, analysis service resource, data analysis service | A web tool, based on a Hidden Markov Model, capable of predicting the transmembrane beta-strands of the gram-negative bacteria outer membrane proteins, and of discriminating such proteins from water-soluble ones when screening large datasets. The model is trained in a discriminative manner, aiming at maximizing the probability of the correct prediction rather than the likelihood of the sequences. The training is performed on a non-redundant database consisting of 16 outer membrane proteins (OMP''s) with their structures known at atomic resolution. We show that we can achieve predictions at least as good comparing with other existing methods, using as input only the amino-acid sequence, without the need of evolutionary information included in multiple alignments. The method is also powerful when used for discrimination purposes, as it can discriminate with a high accuracy the outer membrane proteins from water soluble in large datasets, making it a quite reliable solution for screening entire genomes. This web-server can help you run a discriminating process on any amino-acid sequence and thereafter localize the transmembrane strands and find the topology of the loops. | protein, hidden markov model, prediction, membrane protein, beta-barrel outer membrane protein, gram-negative bacteria, topology, outer membrane protein, beta-barrel protein, probability, transmembrane strand, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
Greek Ministry of National Education and Religious Affairs | PMID:15215419 PMID:15070403 |
Acknowledgement requested | biotools:pred-tmbb, nlx_151734 | https://bio.tools/pred-tmbb | SCR_006190 | PRED-TMBB: A Hidden Markov Model method capable of predicting and discriminating beta-barrel outer membrane proteins | 2026-07-30 09:27:19 | 54 | ||||
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mitopred Resource Report Resource Website 1+ mentions |
mitopred (RRID:SCR_006135) | MITOPRED | service resource, production service resource, analysis service resource, data analysis service | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It predicts nuclear-encoded mitochondrial proteins from all eukaryotic species including plants. Prediction is based on the occurrence patterns of Pfam domains (version 16.0) in different cellular locations, amino acid composition and pI value differences between mitochondrial and non-mitochondrial locations. Additionally, you may download MITOPRED predictions for complete proteomes. Re-calculated predictions are instantly accessible for proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Homo sapiens, Mus musculus and Arabidopsis species as well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases. Queries, at different confidence levels, can be made through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a local file with such accession numbers; (iii) entering protein sequences; (iv) uploading a local file containing protein sequences in FASTA format. The Mitopred algorithm works based on the differences in the Pfam domain occurrence patters and amino acid composition differences in different cellular compartments. Location specific Pfam domains have been determined from the entire eukaryotic set of Swissprot database. Similarly, differences in the amino acid composition between mitochondrial and non-mitochondrial sequences were pre-calculated. This information is used to calculate location-specific amino acid weights that are used to calculate amino acid score. Similarly, pI average values of the N-terminal 25 residues in different cellular location were also determined. This knowledge-base is accessed by the program during execution. | yeast, c. elegans, drosophila, mouse, human, arabidopsis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University at Albany; New York; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mitopred, nif-0000-03956, BioTools:mitopred | https://bio.tools/mitopred, https://bio.tools/mitopred, https://bio.tools/mitopred | SCR_006135 | A genome-scale method for predicting mitochondrial proteins | 2026-07-30 09:27:19 | 7 | ||||||
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Kismeth Resource Report Resource Website 50+ mentions |
Kismeth (RRID:SCR_005444) | Kismeth | service resource, production service resource, analysis service resource, data analysis service | 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 | 2026-07-30 09:27:09 | 53 | ||||||
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GeneTrail Resource Report Resource Website 100+ mentions |
GeneTrail (RRID:SCR_006250) | GeneTrail | service resource, production service resource, analysis service resource, data analysis service | A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathway, microarray, enrichment, genomic, proteomic, function, transcription factor, genomic localization, protein-protein interaction, coiled-coil domain, granzyme-b clevage site, motif, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: TRANSPATH is related to: TRANSFAC is related to: Gene Ontology has parent organization: Saarland University; Saarbrucken; Germany |
PMID:17526521 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:genetrail, OMICS_02236 | https://bio.tools/genetrail | SCR_006250 | 2026-07-30 09:27:21 | 106 | ||||||
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Magic Resource Report Resource Website 500+ mentions |
Magic (RRID:SCR_006406) | MAGIC | data or information resource, database, service resource | Web based interface for exploring and analyzing a comprehensive maize-specific cross-platform expression compendium. This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress. | gene expression, microarray, development stage, annotation, line, perturbation, gene, contrast, pathway, locus tag, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Expression Omnibus is related to: ArrayExpress is related to: Plant Ontology is related to: Gene Ontology has parent organization: Ghent University; Ghent; Belgium |
PMID:24407224 | biotools:magic, OMICS_02206 | https://bio.tools/magic | SCR_006406 | MAGIC - MAize Gene expressIon Compendium, MAize Gene expressIon Compendium | 2026-07-30 09:27:23 | 706 | ||||||
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Pedigree-Draw Resource Report Resource Website 1+ mentions |
Pedigree-Draw (RRID:SCR_008302) | software resource, software application, commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software) | gene, genetic, genomic, macos, bio.tools |
is listed by: Genetic Analysis Software is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154520, OMICS_00213, SCR_010795 | SCR_008302 | PEDIGREE/DRAW | 2026-07-30 09:27:54 | 1 | ||||||||
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COILS: Prediction of Coiled Coil Regions in Proteins Resource Report Resource Website 100+ mentions |
COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) | software resource, software application, data processing software | COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. | software, prediction, database, sequence, coil, globular, protein, probability, bio.tools, FASEB list |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1126/science.252.5009.1162 | biotools:ncoils, OMICS_07850, nif-0000-30263 | https://bio.tools/ncoils, https://sources.debian.org/src/ncoils/ | https://sources.debian.org/src/ncoils/ | SCR_008440 | COILS Server | 2026-07-30 09:27:48 | 164 | ||||||
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SeqExpress Resource Report Resource Website |
SeqExpress (RRID:SCR_007075) | software resource, software application, data processing software | A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options. | gene, gene expression, function, analysis, visualization, statistical analysis, windows, c#, gene function, chromosome location, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Gene Expression Omnibus |
PMID:14988116 | Free | nlx_149285, biotools:seqexpress | https://bio.tools/seqexpress | SCR_007075 | 2026-07-30 09:27:35 | 0 | |||||||
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epigenomix Resource Report Resource Website 1+ mentions |
epigenomix (RRID:SCR_006407) | epigenomix | software resource, software application, data processing software | Software package for the integrative analysis of microarray based gene expression and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types. | epigenetic, gene expression, microarray, histone modification, chip-seq, classification, differential expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24403540 | GNU Lesser General Public License, v3 | biotools:epigenomix, OMICS_02205 | https://bio.tools/epigenomix | SCR_006407 | epigenomix - Epigenetic and gene expression data normalization and integration with mixture models | 2026-07-30 09:27:22 | 2 | |||||
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Assisted Model Building with Energy Refinement (AMBER) Resource Report Resource Website 1000+ mentions |
Assisted Model Building with Energy Refinement (AMBER) (RRID:SCR_014230) | AMBER | simulation software, software resource, software application, standalone software | Software package of molecular simulation programs. It is distributed into AmberTools15 and Amber14. AmberTools15 is a software package which can carry out complete molecular dynamics simulations with either explicit water or generalized Born solvent models. It is distributed in source code format and must be compiled in order to be used. Amber14 builds on AmberTools15 by adding the pmemd program, which provides better performance on multiple CPUs and dramatic speed improvements on GPUs compared to sander (molecular dynamics). GPU info, manuals, and tutorials are available on the website. | molecular simulation, simulation software, software package, molecular dynamics, pmemed, sander, bio.tools |
is listed by: bio.tools is listed by: Debian |
Acknowledgement requested | biotools:amber | https://bio.tools/amber | SCR_014230 | Assisted Model Building with Energy Refinement | 2026-07-30 09:29:06 | 4032 | ||||||
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Subread Resource Report Resource Website 1000+ mentions |
Subread (RRID:SCR_009803) | software resource, software application, data processing software | Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread. | read alignment, DNA-seq reads mapping, RNA-seq reads mapping, mutation discovery, , bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Rsubread has parent organization: University of Melbourne; Victoria; Australia |
Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support ; Australian Government |
PMID:23558742 | Free, Freely available | OMICS_01255, biotools:subread | https://bio.tools/subread, https://sources.debian.org/src/subread/ | SCR_009803 | 2026-07-30 09:28:21 | 1854 | ||||||
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GSA-SNP Resource Report Resource Website 10+ mentions |
GSA-SNP (RRID:SCR_013109) | GSA-SNP | software resource, software application, data processing software | A tool for the gene-set (or pathway) analysis of a genome-wide association study result. It accepts a genome-wide list of SNPs and their association P-values. It summarizes the SNP P-values into nearby genes. The gene-by-gene summary results are then further summarized by gene-sets such as Gene Ontology, KEGG pathways, or user-created gene-sets. Various standardization and statistical tests can be performed and the resulting gene-sets that pass a significance level after multiple-testing correction are reported. The tool is written in Java and is available as a standalone version. | clinical neuroinformatics, computational neuroscience, imaging genomics, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: Soongsil University; Seoul; South Korea |
PMID:20501604 | GNU General Public License v2 | nlx_155765, biotools:gsa-snp | https://bio.tools/gsa-snp | SCR_013109 | 2026-07-30 09:28:52 | 18 | ||||||
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Trim Galore Resource Report Resource Website 5000+ mentions Rating or validation data |
Trim Galore (RRID:SCR_011847) | Trim Galore! | software resource, software application, data processing software | Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data. | Automate, quality, adapter, trimming, remove, biased, methylation, position, RRBS, reduced, representation, bisulfite, data, sequence, wrapper, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute works with: cutadapt |
Free, Available for download, Freely available | biotools:trim_galore, OMICS_01096, SCR_016946 | https://github.com/FelixKrueger/TrimGalore, https://bio.tools/trim_galore, https://sources.debian.org/src/trim-galore/ | SCR_011847 | TrimGalore | 2026-07-30 09:28:42 | 6255 | ||||||
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docker4seq Resource Report Resource Website 1+ mentions |
docker4seq (RRID:SCR_017006) | software resource, software application, data processing software | Software R package to execute next generation sequencing computing applications, e.g. reads mapping and counting, wrapped in docker containers. | next, generation, sequencing, computing, application, read, mapping, count, docker, container, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: University of Turin;Turin;Italy |
Free, Available for download, Freely available | biotools:docker4seq | https://kendomaniac.github.io/docker4seq/index.html, https://bio.tools/docker4seq | SCR_017006 | 2026-07-30 09:30:08 | 5 |
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