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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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zAlign Resource Report Resource Website |
zAlign (RRID:SCR_024360) | aligment software | Software tool as local sequence aligner intended for use with large biological DNA sequences, with more than 1 Millions of base pairs. | sequence aligner, large biological DNA sequences, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21299 | https://sources.debian.org/src/zalign/ | SCR_024360 | zalign | 2026-08-01 12:08:16 | 0 | |||||||
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mzMatch Resource Report Resource Website 1+ mentions |
mzMatch (RRID:SCR_000543) | software toolkit, software resource | A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java. | metabolomics, analysis, java, tool, peak extraction, filtering, normalization, derivative detection, identification, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23162054 | Free, Available for download, Freely available, | biotools:mzmatch, OMICS_02642 | https://bio.tools/mzmatch | SCR_000543 | 2026-08-02 09:02:53 | 5 | |||||||
|
Bioinformatics Toolkit Resource Report Resource Website 100+ mentions |
Bioinformatics Toolkit (RRID:SCR_010277) | software toolkit, software resource | A platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house, and serveral public tools are offered with extended functionality. Most frequently used tools HHpred Sensitive protein homology detection and structure prediction by HMM-HMM-comparison. Starting from a query sequence, HHpred builds a multiple sequence alignment using HHblits and turns it into a profile HMM. This is then compared it with a database of HMMs representing proteins with known structure (e.g. PDB, SCOP) or annotated protein families (e.g. PFAM, SMART, CDD, COGs, KOGs). The output is a list of closest homologs with alignments. HHpred can also build 3d homology models using the identified templates in the PDB database. It can optimize template picking and query-template alignments for homology modeling. The HHblits software is part of the open source package HHsuite. HHblits Remote homology detection method based on iterative HMM-HMM comparison. HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and iteratively searches through uniprot20 or nr20 databases by adding significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. The HHblits software is part of the open source package HHsuite. Quick2d Quick2D gives you an overview of secondary structure features like alpha-helices, extended beta-sheets, coiled coils, transmembrane helices and disorder regions. Predictions by PSIPRED, JNET, Prof(Rost), Prof(Ouali), Coils, MEMSAT2, HMMTOP, DISOPRED2 and VSL2. Modeller A Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Coils/PCoils This server compares a single sequence (COILS) or a sequence alignment (PCOILS) to a database of known coiled-coils and derives a similarity score. The program then calculates the probability that the sequence will adopt a coiled-coil conformation. PSI-Blast Search with an amino acid sequence against protein databases for locally similar sequences. Similar to ProteinBLAST but more sensitive. PSI-BLAST first performs a BLAST search and builds an alignment from the best local hits. This alignment is then used as a query for the next round of search. After each successive round the search alignment is updated. | bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
DOI:10.1038/NMETH.1818 | nlx_156936, OMICS_28407, biotools:bioinformatics_toolkit | https://bio.tools/bioinformatics_toolkit, https://sources.debian.org/src/hhsuite/ | SCR_010277 | 2026-08-02 09:05:41 | 235 | ||||||||
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VISTA Browser Resource Report Resource Website 50+ mentions |
VISTA Browser (RRID:SCR_011808) | software toolkit, software resource | Software tools for comparative genomics.Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species. | Comparative genomics tools, genomic sequences, comparative analysis, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
Office of Biological and Environmental Research ; Office of Science ; US Department of Energy ; NHLBI |
PMID:15215394 | Free, Freely available | OMICS_00948, biotools:vista | http://genome.lbl.gov/vista/index.shtml, https://bio.tools/vista | SCR_011808 | VISTA, vista | 2026-08-02 09:06:03 | 87 | |||||
|
HTQC Resource Report Resource Website 10+ mentions |
HTQC (RRID:SCR_006448) | HTQC | software toolkit, software resource | A software toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc.. | c++, illumina, command-line |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:23363224 DOI:10.1186/1471-2105-14-33 |
GNU General Public License, v3 | OMICS_01052 | https://sources.debian.org/src/htqc/ | SCR_006448 | HTQC - Quality control and filtration for illumina sequencing data | 2026-08-02 09:04:55 | 42 | |||||
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Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software toolkit, software resource | Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. | hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probability |
is listed by: Debian is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG006399; NIMH R01 MH101244; NHGRI F32HG007805; Wellcome Trust WT098051; Austrian Science Fund J-3401; NHGRI HG007022; NHLBI HL117626; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NWO 480-05-003; Dutch Brain Foundation |
PMID:27694958 PMID:27270109 |
Free, Available for download, Freely available | OMICS_14099, SCR_017262 | https://sources.debian.org/src/bio-eagle/, https://github.com/poruloh/Eagle, https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ | SCR_015991 | Bio-eagle, Eagle1, Eagle2 | 2026-08-02 09:07:16 | 51 | |||||
|
MultiQC Resource Report Resource Website 1000+ mentions |
MultiQC (RRID:SCR_014982) | data access protocol, software resource | Data aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python. | bioinformatics, data aggregate, python, open source, html report, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Science for Life Laboratory ; National Genomics Infrastructure |
PMID:27312411 DOI:10.1093/bioinformatics/btw354 |
Open source, Available for download | biotools:multiqc, OMICS_12426 | https://github.com/ewels/MultiQC https://pypi.python.org/pypi/multiqc, https://bio.tools/multiqc, https://sources.debian.org/src/multiqc/ | SCR_014982 | 2026-08-02 09:07:05 | 3098 | ||||||
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topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software toolkit, software resource | Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. | r, go, go graph, local similarities, software tool, software package, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite works with: Gene Ontology is hosted by: Bioconductor |
Available for download | biotools:topgo | https://bio.tools/topgo | SCR_014798 | 2026-08-02 09:06:40 | 2839 | ||||||||
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DANPOS2 Resource Report Resource Website 100+ mentions |
DANPOS2 (RRID:SCR_015527) | software toolkit, software resource | Software toolkit with various functions for the analysis of nucleosome and protein occupancy by sequencing. | nucleosome analysis, protein analysis, protein occupancy, bio.tools |
uses: Dpos is listed by: bio.tools is listed by: Debian |
Available for download, Different versions are available for download | biotools:danpos | https://bio.tools/danpos | SCR_015527 | DANPOS | 2026-08-02 09:06:57 | 111 | |||||||
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HASTE-project Resource Report Resource Website 1+ mentions |
HASTE-project (RRID:SCR_020932) | software toolkit, software resource | Software toolkit for rapid development of cloud native intelligent data pipelines for scientific data streams. Hierarchical approach to acquisition, analysis, and interpretation of image data. Developed in the project Hierarchical Analysis of Spatial and Temporal Data. | Intelligent data pipelines development, intelligent spatial hierarchies, temporal information hierarchies, distributing data, data streams, image data hierarchical approach, image data, hierarchical analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:haste_toolkit | https://bio.tools/haste_toolkit | SCR_020932 | HASTE Toolkit, Hierarchical Analysis of Spatial and TEmporal data, Hierarchical Analysis of Spatial and Temporal Data | 2026-08-02 09:08:01 | 1 | |||||||
|
MERMAID Resource Report Resource Website |
MERMAID (RRID:SCR_020939) | software toolkit, software resource | Registration toolbox written in pyTorch. Supports various image registration methods. Focuses on nonparametric registration approaches including stationary velocity fields and large discplacement diffeomorphic metric mapping models though simple affine registration is also possible. Allows for rapid prototyping of new image registration approaches and similarity measures. | Image registration, nonparametric registration, rapid prototyping, new image registration, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Jupyter Notebook |
Free, Available for download, Freely available | biotools:MERMAID | https://github.com/uncbiag/mermaid/blob/master/docs/source/index.rst, https://bio.tools/MERMAID | SCR_020939 | iMagE Registration via autoMAtIc Differentiation | 2026-08-02 09:08:01 | 0 | |||||||
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scVelo Resource Report Resource Website 100+ mentions |
scVelo (RRID:SCR_018168) | software toolkit, software resource | Software package for estimating and analyzing RNA velocities in single cells using dynamical modeling. RNA Velocity using dynamical modeling. | RNA veloscity, analysis, single cell, dynamic modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:scVelo | https://scvelo.readthedocs.io/, https://bio.tools/scVelo | SCR_018168 | scvelo, single-cell RNA Velocity generalized to transient cell states | 2026-08-02 09:07:46 | 199 | |||||||
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GTDB-Tk Resource Report Resource Website 50+ mentions |
GTDB-Tk (RRID:SCR_019136) | software toolkit, software resource | Open source software tool for assigning objective taxonomic classifications to bacterial and archaeal genomes based on Genome Database Taxonomy. Designed to work with recent advances that allow metagenome assembled genomes to be obtained directly from environmental samples. Can also be applied to isolate and single cell genomes. | Assigning objective taxonomic classifications, bacterial genome, archaeal genome, Genome Database Taxonomy, metagenome assembled genome, environmental sample, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:GtDb-tk | https://bio.tools/GTDB-Tk | SCR_019136 | GTDB-Tk v1.3.0, Genome Database Taxonomy-Tk | 2026-08-02 09:07:57 | 79 | |||||||
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ensembldb Resource Report Resource Website 10+ mentions |
ensembldb (RRID:SCR_019103) | software toolkit, software resource | Software R package to create and use Ensembl based annotation resources. | Ensembl based annotation, Ensembl, annotation, create annotation, use annotation, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:30689724 | Free, Available for download, Freely available | biotools:ensembldb | https://github.com/jorainer/ensembldb, https://bio.tools/ensembldb | SCR_019103 | ensembldb v2.6.8 | 2026-08-02 09:08:05 | 10 | ||||||
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clustLasso Resource Report Resource Website 1+ mentions |
clustLasso (RRID:SCR_018820) | software toolkit, software resource | Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach. | Predictive signatures, microbial phenotype, cluster lasso approach, build predictive signature, phenotype, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:clustlasso | https://bio.tools/clustlasso | SCR_018820 | 2026-08-02 09:07:53 | 1 | ||||||||
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Spot Resource Report Resource Website 100+ mentions |
Spot (RRID:SCR_018915) | software toolkit, software resource | Open source software tool for file based localization of numerical perturbations in data analysis pipelines. Identifies components in pipeline, at resolution level of system process, that produce different results in different execution conditions. | Numerical perturbation, reproducibility, numerical differences, operating systems, neuroimaging pipeline stability, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available, Available for download | DOI:10.5281/zenodo.3873219, biotools:spottool | https://bio.tools/spottool | SCR_018915 | Spot: File-based localization of numerical perturbations in data analysis pipelines | 2026-08-02 09:07:54 | 141 | |||||||
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Genomic Annotation in Livestock for positional candidate LOci Resource Report Resource Website 10+ mentions |
Genomic Annotation in Livestock for positional candidate LOci (RRID:SCR_019212) | GALLO | software toolkit, software resource | Software R package developed for accurate annotation of genes and quantitative trait loci located in regions identified in common genomic analyses performed in livestock, such as Genome Wide Association Studies and transcriptomics using RNA-Sequencing. Allows graphical visualization of gene and QTL annotation results, data comparison among different grouping factors like methods, breeds, tissues, statistical models, studies and QTL enrichment in different livestock species including cattle, pigs, sheep, and chickens. | QTLs, multi-omics integration, qtl annotation, gene annotation, datamining, qtl enrichment analysis, livestock, bio.tools |
is listed by: CRAN is listed by: bio.tools is listed by: Debian has parent organization: University of Guelph; Ontario; Canada |
Free, Freely available | biotools:genomic_annotation_in_livestock_for_positional_candidate_loci_gallo | https://bio.tools/genomic_annotation_in_livestock_for_positional_candidate_loci_gallo | SCR_019212 | 2026-08-02 09:08:06 | 14 | |||||||
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SMI Services Resource Report Resource Website 1+ mentions |
SMI Services (RRID:SCR_018881) | SMI Services | software toolkit, software resource | Software suite of tools for cataloguing and anonymising DICOM files, as used for Scottish Medical Imaging project. Software suite of microservices for loading, anonymising, linking and extracting large volumnes of dicom medical images to support medical research. Platform allows dicom tags extracted from clinical images to be loaded into MongoDB and relational database tables for purposes of generating anonymous linked research extracts including image anonymisation. | Database management system, anonymising DICOM files, cataloguing DICOM files, medical image, DICOM medical image, image anonymisation, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:smi_services | https://bio.tools/smi_services | SCR_018881 | Scottish Medical Imaging Services | 2026-08-02 09:07:53 | 1 | ||||||
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psych Resource Report Resource Website 10+ mentions |
psych (RRID:SCR_021744) | software toolkit, software resource | Software R package for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis.Procedures for Psychological, Psychometric, and Personality Research. Used for personality, psychometric theory and experimental psychology. | Psychological research procedure, Psychometric research procedure, Personality research procedure, factor analysis, principal component analysis, cluster analysis, reliability analysis |
is listed by: CRAN is listed by: Debian |
Free, Available for download, Freely available | https://personality-project.org/r/psych/, https://sources.debian.org/src/r-cran-psych/ | SCR_021744 | 2026-08-02 09:08:16 | 43 | |||||||||
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Mammalian Gene Collection Resource Report Resource Website 10+ mentions |
Mammalian Gene Collection (RRID:SCR_007024) | MGC | cell repository, material resource, biomaterial supply resource | NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | cell line, cdna, frozen, clone, vector, gene, open reading frame, sequence, expressed sequence tag, bio.tools, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: One Mind Biospecimen Bank Listing is related to: NIDDK Information Network (dkNET) is related to: ATCC is related to: GenBank is related to: Invitrogen Clones is related to: Open Biosystems is related to: Zebrafish Gene Collection has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research | Free, Freely available | biotools:mammalian_gene_collection, nif-0000-00195 | https://bio.tools/mammalian_gene_collection | SCR_007024 | Mammalian Gene Collection | 2026-08-04 09:41:44 | 46 |
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