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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MAFFT Resource Report Resource Website 10000+ mentions |
MAFFT (RRID:SCR_011811) | MAFFT | software resource, alignment software, image analysis software, software toolkit, data processing software, software application | Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments. | alignment, amino acid, nucleotide, sequence, DNA, sequence alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
EMBL ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:12136088 PMID:17118958 PMID:16362903 PMID:15661851 PMID:18439255 PMID:23023983 DOI:10.1093/bib/bbn013 |
biotools:MAFFT, OMICS_00979 | https://www.ebi.ac.uk/Tools/msa/mafft/, https://www.genome.jp/tools-bin/mafft, https://myhits.isb-sib.ch/cgi-bin/mafft, https://bio.tools/MAFFT, https://sources.debian.org/src/mafft/ | SCR_011811 | Multiple Alignment using Fast Fourier Transform, MAFFT version 5, MAFFT version 7 | 2026-08-06 09:27:50 | 22450 | |||||
|
ProDesign Resource Report Resource Website 10+ mentions |
ProDesign (RRID:SCR_010966) | ProDesign | software resource, service resource, production service resource, data analysis service, analysis service resource | Webserver that can be used to find oligonucleotide probe sets for microarray slides. The probes can be for individual sequences or for clusters of genes. This webserver accepts files up to 200 kb in size in order to minimize the running time. For larger files please download the program. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:17392329 | Licensed free of charge for academic use | OMICS_00837, biotools:prodesign | https://bio.tools/prodesign | SCR_010966 | 2026-08-06 09:27:41 | 19 | ||||||
|
Genome Projector Resource Report Resource Website 1+ mentions |
Genome Projector (RRID:SCR_011790) | Genome Projector | software resource, service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | A searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk. | genome, plasmid, pathway, dna, map, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Japan Society for the Promotion of Science | GNU General Public License, V.2 | OMICS_00912, biotools:genome_projector | https://bio.tools/genome_projector | SCR_011790 | 2026-08-06 09:27:50 | 3 | ||||||
|
METAREP Resource Report Resource Website 1+ mentions |
METAREP (RRID:SCR_011926) | METAREP | data analysis software, software application, software resource, data processing software | A tool for high-performance comparative metagenomics that allows users to view, query, browse, and compare metagenomics annotation profiles from short reads or assemblies. Users can use statistical tests, hierarchical clustering, multidimensional scaling, and heat maps to compare multiple datasets at various functional and taxonomic levels. | microbiome, comparison, comparative metagenomics, annotation, short read, short assembly, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: J. Craig Venter Institute |
DOI:10.1093/bioinformatics/btq455 | Open source | biotools:metarep, OMICS_01480 | https://bio.tools/metarep | SCR_011926 | 2026-08-06 09:27:50 | 8 | ||||||
|
PlnTFDB Resource Report Resource Website 100+ mentions |
PlnTFDB (RRID:SCR_010899) | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | Public database arising from efforts to identify and catalogue all plant genes involved in transcriptional control.Integrative plant transcription factor database that provides web interface to access large sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. Provides access point to its daughter databases of species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags, domain architecture and scientific literature is provided for each family. | protein model, protein sequence, gene family, protein, transcriptional control, blast, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
University of Potsdam ; Germany ; German Federal Ministry of Education and Research ; Fond der Chemischen Industrie |
PMID:19858103 PMID:17286856 |
Free, Freely available | biotools:plntfdb, OMICS_00561 | http://plntfdb.bio.uni-potsdam.de/v3.0/, https://bio.tools/plntfdb | SCR_010899 | Plant Transcription Factor Database, PlnTFDB v3.0 | 2026-08-06 09:27:41 | 201 | |||||
|
CPFP Resource Report Resource Website 1+ mentions |
CPFP (RRID:SCR_012043) | data analysis software, software application, software resource, data processing software | Software providing a data analysis pipeline for shotgun mass-spectrometry proteomics. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: University of Oxford; Oxford; United Kingdom |
PMID:20189941 | OMICS_02448, biotools:cpfp | https://bio.tools/cpfp | SCR_012043 | Central Proteomics Facilities Pipeline | 2026-08-06 09:27:50 | 7 | |||||||
|
Orientations of Proteins in Membranes database Resource Report Resource Website 100+ mentions |
Orientations of Proteins in Membranes database (RRID:SCR_011961) | OPM | image collection, database, data or information resource | Database that provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal. | protein, membrane, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan; Ann Arbor; USA |
NSF | PMID:16397007 | Acknowledgement requested | OMICS_01612, biotools:opm | https://bio.tools/opm | SCR_011961 | Orientations of Proteins in Membranes (OPM) database, OPM Database | 2026-08-06 09:27:49 | 120 | ||||
|
VisSR Resource Report Resource Website 1+ mentions |
VisSR (RRID:SCR_012024) | VisSR | data visualization software, software application, software resource, data processing software | Software to generate a visual representation of sRNAs and user-imported genomic features. The tool may be run on its own or from other tools, e.g. miRCat. |
is listed by: OMICtools is listed by: UEA sRNA Workbench is listed by: bio.tools is listed by: Debian has parent organization: University of East Anglia; Norwich; United Kingdom |
OMICS_02107, biotools:vissr | https://bio.tools/vissr | SCR_012024 | Visualisation of sRNAs | 2026-08-06 09:27:50 | 3 | ||||||||
|
kmer-SVM Resource Report Resource Website 1+ mentions |
kmer-SVM (RRID:SCR_010882) | kmer-SVM | software resource, service resource, production service resource, data analysis service, analysis service resource | A webserver built on the Galaxy framework that enables the mining of sequence data for transcription factor binding sites. This tool suite was designed to aid in analysis of next-generation sequencing (NGS) data that uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. While you may use datasets already available from Galaxy, you can upload your data using the ''Get Data'' Tool. The tool can upload data from a variety of locations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA has parent organization: Galaxy |
PMID:23771147 | Acknowledgement requested | OMICS_00484, biotools:kmer-svm | https://bio.tools/kmer-svm | SCR_010882 | 2026-08-06 09:27:45 | 3 | ||||||
|
PAML Resource Report Resource Website 1000+ mentions |
PAML (RRID:SCR_014932) | PAML | software resource, data analysis software, software toolkit, data processing software, software application | Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML estimates parameters and tests hypotheses to study the evolutionary process from a phylogenetic tree., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | phylogenetic analysis, dna, protein sequences, evolutionary process, estimate parameters, test hypothesis, maximum likelihood, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at Berkeley; Berkeley; USA works with: PAUP works with: PHYLIP works with: PhyML works with: RAxML |
PMID:9367129 DOI:10.1093/molbev/msm088 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04238, biotools:paml | https://bio.tools/paml, https://sources.debian.org/src/paml/ | SCR_014932 | Phylogenetic Analysis by Maximum Likelihood, Phylogenetic Analysis by Maximum Likelihood (PAML) | 2026-08-06 09:28:29 | 4930 | |||||
|
CHiCAGO Resource Report Resource Website 100+ mentions |
CHiCAGO (RRID:SCR_014941) | software resource, data analysis software, software toolkit, data processing software, software application | Statistical pipeline for detecting significant chromosomal interactions in Capture Hi-C data. CHiCAGO uses a convolution background model accounting for both random Brownian collisions between chromatin fragments and technical noise. CHiCAGO then performs a p-value weighting procedure based on the expected true positive rates at different distance ranges, with scores representing soft-thresholded -log weighted p-values., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | capture hi-c, capture hi-c data, chic, brownian collisions, chromatin, p-value weighting, genomic organization, genome, statistical analysis, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Babraham Institute |
BBSRC ; MRC UK ; EMBL |
PMID:27306882 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:chicago | https://bitbucket.org/chicagoTeam/chicago, https://bio.tools/chicago | SCR_014941 | Capture HiC Analysis of Genomic Organisation, Capture HiC Analysis of Genomic Organization, CHiCAGO: Capture HiC Analysis of Genomic Organisation | 2026-08-06 09:28:26 | 163 | |||||
|
SOAPnuke Resource Report Resource Website 1000+ mentions |
SOAPnuke (RRID:SCR_015025) | sequence analysis software, software resource, data analysis software, data processing software, software application | Multi-threaded software for rapid quality control and preprocessing of high throughput sequencing data specified for different experiments. It consists of four modules that speed up the report on statistics graphs of raw datasets, preprocessed datasets and preprocessing status. | sequence data, fastq, dge dataset, rna, metagenomics, bio.tools |
is listed by: SOAP is listed by: bio.tools is listed by: Debian |
Open Source, Free | biotools:soapnuke | https://bio.tools/soapnuke | SCR_015025 | 2026-08-06 09:28:27 | 1447 | ||||||||
|
Bowtie 2 Resource Report Resource Website 1000+ mentions |
Bowtie 2 (RRID:SCR_016368) | sequence analysis software, software resource, image analysis software, alignment software, data analysis software, data processing software, software application | Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method. | sequence, analysis, long, reference, sequence, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools |
is used by: HLA-HD is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Bowtie |
NHGRI R01 HG006102; NIGMS R01 GM083873 |
PMID:22388286 | Free, Available for download, Freely available | biotools:bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml, https://github.com/BenLangmead/bowtie2, https://bio.tools/bowtie2 | SCR_016368 | , bowtie 2, bowtie2 v 2.2.3 | 2026-08-06 09:28:25 | 1745 | |||||
|
Off-Spotter Resource Report Resource Website 10+ mentions |
Off-Spotter (RRID:SCR_015739) | web application, algorithm resource, software resource | Web application that identifies genomic instances for a given combination of gRNA(s), PAM, number of mismatches, and seed. This tool is limited to a single 1,000 nucleotides sequence or fewer than twenty CR-separated 20-mers. | CRISPR, Cas, sgrna, prokaryotic immune system, genetic engineering, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Thomas Jefferson University; Pennsylvania; USA |
William M. Keck Foundation | PMID:25630343 | Freely available, Free, Available for download, Tutorial available | biotools:off-spotter | https://bio.tools/off-spotter | SCR_015739 | Off-Spotter: tool for CRISPR/Cas design, Off-spotter sgRNA algorithm | 2026-08-06 09:28:41 | 43 | |||||
|
GEN3VA Resource Report Resource Website 1+ mentions |
GEN3VA (RRID:SCR_015682) | data analysis software, software application, software resource, data processing software | Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme. | GEO2Enrichr, gene expression signatures, enrichment analyses, multiple studies, biological theme, bio.tools |
is listed by: bio.tools is listed by: Debian works with: Gene Expression Omnibus (GEO) |
NHLBI U54 HL127624; NCI U54 CA189201; NIGMS R01 GM098316 |
PMID:27846806 | Free, Freely available | biotools:gen3va | https://github.com/MaayanLab/gen3va, https://bio.tools/gen3va | SCR_015682 | GENE Expression and Enrichment Vector Analyzer | 2026-08-06 09:28:42 | 5 | |||||
|
BCBtoolkit Resource Report Resource Website 50+ mentions |
BCBtoolkit (RRID:SCR_015519) | software resource, data analysis software, software toolkit, data processing software, software application | Software toolkit that provides several multi-modal tools to assess brain disconnections and remote effects of lesions. All modules are designed to process brain lesion data with a normalization algorithm, a module to estimate the probability and the severity of white matter disconnections, and a tool to build a map of the disconnected areas. | brain lesion, brain disconnection, white matter, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: NIH Human Connectome Project |
Open source, Free, Available for download, Available on Mac OS, Available on Linux | biotools:bcbtoolkit | https://bio.tools/bcbtoolkit | SCR_015519 | BCBtoolkit 4.0 | 2026-08-06 09:28:39 | 58 | |||||||
|
Atac Resource Report Resource Website 1000+ mentions |
Atac (RRID:SCR_015980) | sequence analysis software, software resource, image analysis software, alignment software, data analysis software, data processing software, software application | Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences. | software, tool, DNA, sequence, analysis, aligning, genome, compare, mapping, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btr285 | Free, Freely available, Available for download | OMICS_29044, biotools:atac | https://bio.tools/atac, https://sources.debian.org/src/atac/ | SCR_015980 | 2026-08-06 09:28:46 | 1748 | |||||||
|
Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | software resource, data analysis software, data management software, software toolkit, data processing software, software application | Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies. | c++, api, sam, bam genome, sequence, alignment, data, analysis, management, command, manipulation, binary, map, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG004719; NHGRI RC2 HG005552 |
PMID:21493652 DOI:10.1093/bioinformatics/btr174 |
biotools:bamtools, OMICS_11315 | https://bio.tools/bamtools, https://sources.debian.org/src/bamtools/ | SCR_015987 | API:Application Programming Interface, BAM:Binary Alignment Map, SAM:Sequence Alignment Map | 2026-08-06 09:28:46 | 324 | ||||||
|
scater Resource Report Resource Website 100+ mentions |
scater (RRID:SCR_015954) | sequence analysis software, software resource, data analysis software, software toolkit, data processing software, data visualization software, software application | Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data. | scRNA-seq, rna, rnaseq, single, cell, analysis, gene, expression, quality, control, preprocessing, normalization, visualization, r, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Health and Medical Research Council of Australia APP1112681; European Molecular Biology Laboratory ; Cancer Research UK A17197; United Kingdom Medical Research Council ; Oxford Single Cell Biology Consortium |
Free, Available for download | biotools:scater | https://bioconductor.org/packages/scater/, https://bio.tools/scater | SCR_015954 | scater (single-cell analysis toolkit for gene expression data in R) | 2026-08-06 09:28:47 | 173 | ||||||
|
ALTER Resource Report Resource Website 100+ mentions |
ALTER (RRID:SCR_015968) | sequence analysis software, software resource, image analysis software, alignment software, data analysis software, data processing software, web application, software application | Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats. | Alignment conversion, genome, sequence, DNA, protein, format alignment, phylogenetics, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
European Research Council ERC-2007-Stg 203161-PHYGENOM to D.P.; Spanish Ministry of Science and Education BFU2009-08611 to D.P.; Xunta de Galicia PGIDIT07PXIB310202PR to D.P.; INBIOMED initiative ; University of Vigo 09VIB10 to F.F-.R. |
PMID:20439312 DOI:10.1093/nar/gkq321 |
Freely available, Free, Available for download | OMICS_19786, biotools:alter | https://github.com/sing-group/ALTER, https://bio.tools/alter, https://sources.debian.org/src/alter-sequence-alignment/ | SCR_015968 | ALTER: ALignment Transformation EnviRonment, ALignment Transformation EnviRonment | 2026-08-06 09:28:47 | 112 |
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