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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PPR-Meta Resource Report Resource Website 1+ mentions |
PPR-Meta (RRID:SCR_016915) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to identify metagenomic sequences of phages, chromosomes or plasmids. Used for identifying phages and plasmids from metagenomic fragments using deep learning., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | identify, metagenomic, sequence, phage, chromosome, plasmid, fragment, machine, learning |
is related to: Python Programming Language is related to: MATLAB is related to: tensorflow |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/zhenchengfang/PPR-Meta | SCR_016915 | 2026-09-05 06:28:15 | 4 | |||||||||
|
seqNMF Resource Report Resource Website 1+ mentions |
seqNMF (RRID:SCR_017068) | data analysis software, data processing software, software application, software resource | Software tool for unsupervised discovery of sequential structure. Used to detect sequences in neural data generated by internal behaviors, such as animal thinking or sleeping. Used for unsupervised discovery of temporal sequences in high dimensional datasets in neuroscience without reference to external markers. | sequence, structure, high, dimention, dataset, neuroscience, repeated, sequential, pattern, data | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | Department of Energy ; Labor and Economic Growth Computational Science Graduate Fellowship ; G Harold and Leila Y. Mathers Foundation ; NIBIB T32 EB019940; NIDCD R01 DC009183; NIMH R25 MH062204; NINDS U19 NS10 4648; Simons Foundation Simons Collaboration for the Global Brain ; U.S. Department of Defense NDSEG Fellowship program |
PMID:30719973 | Free, Available for download, Freely available | SCR_017068 | 2026-09-05 06:28:18 | 6 | ||||||||
|
rnaSPAdes Resource Report Resource Website 50+ mentions |
rnaSPAdes (RRID:SCR_016992) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9. | assembling, transcript, RNA-Seq, data, single, cell, genome, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: SPAdes is related to: rnaQUAST |
Russian Science Foundation 14-50-00069 | DOI:10.1101/420208 | Free, Available for download, Freely available | biotools:rnaSPAdes_autogenerated | https://bio.tools/rnaSPAdes_autogenerated | SCR_016992 | 2026-09-05 06:28:16 | 58 | ||||||
|
Clustal 2 Resource Report Resource Website 1000+ mentions |
Clustal 2 (RRID:SCR_017055) | alignment software, data processing software, data visualization software, image analysis software, software application, software resource | Software tool for nucleotide sequence alignment. Graphical version of multiple sequence alignment program for DNA and proteins. Windows interface for ClustalW multiple sequence alignment program. Provides integrated environment for performing multiple sequence and profile alignments and analyzing results. Available on Linux, Mac and Windows. | graphical, multiple, sequence, alignment, DNA, protein |
is related to: Clustal W2 is related to: Clustal Omega |
CNRS ; EMBL ; INSERM ; Ministère de la Recherche et Technologie ; Science Foundation Ireland |
PMID:17846036 PMID:9396791 |
Free, Available for download, Freely available | biotools:clustal2 | http://www.clustal.org/download/clustalx_help.html, https://bio.tools/clustal2 | SCR_017055 | Clustalx, CLUSTAL_X, clustalx, clustal X, clustal2 | 2026-09-05 06:28:17 | 1535 | |||||
|
Nuclear Hormone Receptor Scan Resource Report Resource Website 1+ mentions |
Nuclear Hormone Receptor Scan (RRID:SCR_016975) | NHR-scan | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web interface for computational prediction of nuclear hormone receptor binding sites in genomic sequences. Flexible Hidden Markov Model framework to allow for variable spacing and orientation of half sites. Allows for parameter modifications. | prediction, nuclear, hormone, receptor, binding, site, genomic, sequence, parameter, modification, analysis | is listed by: OMICtools | Canadian Institutes of Health Research ; Pharmacia Corporation to the Center for Genomics and Bioinformatics |
PMID:15563547 | Free, Available, Acknowledgement requested | OMICS_14042 | SCR_016975 | NHR-scan, NHR Scan, NHRScan, Nuclear Hormoe Receptor Scan | 2026-09-05 06:28:16 | 5 | |||||
|
EMBOSSMatcher Resource Report Resource Website 10+ mentions |
EMBOSSMatcher (RRID:SCR_017252) | alignment software, data access protocol, data processing software, image analysis software, software application, software resource, web service | Software tool for pairwise sequence alignment. Identifies local similarities in two input sequences. One of EMBL-EBI search and sequence analysis tools. | pairwise, sequence, alignment, identify, local, similarity, two, input, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools |
EMBL | PMID:30976793 | Free, Freely available | biotools:ebi_search | https://bio.tools/ebi_search | SCR_017252 | EMBOSS Matcher, emboss_matcher, EMBOSS_Matcher | 2026-09-05 06:28:21 | 16 | |||||
|
Juicer Resource Report Resource Website 100+ mentions |
Juicer (RRID:SCR_017226) | data analysis software, data processing software, software application, software resource | Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps. | analysis, kilobase, resolution, Hi-C, data, terabase, dataset, transform, raw, sequence, normalized, contact, map | has parent organization: Baylor College of Medicine; Houston; Texas | Cancer Prevention Research Institute of Texas ; Google Research Award ; IBM University Challenge Award ; McNair Medical Institute Scholar Award ; NHGRI HG003067; NHGRI HG006193; NHLBI U01 HL130010; NIH Office of the Director DP2 OD008540; NSF PHY-1427654; NVIDIA Research Center Award ; PD Soros Fellowship ; President Early Career Award in Science and Engineering ; Welch Foundation |
PMID:27467249 | Free, Available for download, Freely available | SCR_017226 | 2026-09-05 06:28:20 | 119 | ||||||||
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PIRATE Resource Report Resource Website 10+ mentions |
PIRATE (RRID:SCR_017265) | data analysis software, data processing software, software application, software resource | Software pangenomics toolbox for clustering diverged orthologues in bacteria. Used to identify and classify orthologous gene families in bacterial pangenomes over wide range of sequence similarity thresholds. | Pangenome, clustering, genomics, bacteria, orthologue, gene, sequence, amino acid, nucleotide, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/598391 | Free, Available for download, Freely available | biotools:PIRAtE | https://bio.tools/PIRATE | SCR_017265 | Pangenome Iterative Refinement And Threshold Evaluation | 2026-09-05 06:28:21 | 23 | ||||||
|
RepeatFiller Resource Report Resource Website 10+ mentions |
RepeatFiller (RRID:SCR_017414) | alignment software, data processing software, image analysis software, software application, software resource | Software tool to incorporate newly detected repeat overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in chains, which makes it feasible to consider all seeds including those that overlap repetitive regions. Used to improve genome alignments by incorporating previously undetected local alignments between repetitive sequences. | Repeat, overlapping, alignment, pairwise, chain, local, genomic, region, colinear, block, sequence, undetected, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany |
DOI:10.1101/696922 | Free, Freely available | biotools:RepeatFiller, BioTools:RepeatFiller | https://bio.tools/RepeatFiller, https://bio.tools/RepeatFiller, https://bio.tools/RepeatFiller | SCR_017414 | 2026-09-05 06:28:24 | 16 | |||||||
|
trimAl Resource Report Resource Website 500+ mentions |
trimAl (RRID:SCR_017334) | data analysis software, data processing software, software application, software resource | Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses. | removal, spurious, sequence, poorly, aligned, region, multiple, alignment, trimming, large, scale, phylogenetic, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
FIS ; MEC |
PMID:19505945 | Free, Available for download, Freely available | biotools:trimal | https://vicfero.github.io/trimal/, https://bio.tools/trimal | SCR_017334 | 2026-09-05 06:28:22 | 673 | ||||||
|
HomoplasyFinder Resource Report Resource Website 1+ mentions |
HomoplasyFinder (RRID:SCR_017300) | data analysis software, data processing software, software application, software resource, software toolkit, standalone software | Software tool to identify and annotate homoplasies on phylogeny and sequence alignment. Used to automatically identify any homoplasies present in simulated and real phylogenetic data. Java application that can be used as standalone tool or within statistical programming environment R. | homoplasy, phylogeny, sequence, alignment, identify, data, annotate | Science Foundation Ireland | PMID:30663960 | Free, Available for download, Freely available | https://github.com/JosephCrispell/homoplasyFinder | SCR_017300 | 2026-09-05 06:28:22 | 6 | ||||||||
|
BEAST2 Resource Report Resource Website 100+ mentions |
BEAST2 (RRID:SCR_017307) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager. | Bayesian, evolutionary, sampling, tree, phylogenic, analysis, Markov, chain, monte carlo, phylogenetic, population, genetic, phylodynamic, sequence |
is related to: BASTA is related to: BEAST is related to: PhyDyn has parent organization: University of Auckland; Auckland; New Zealand |
EMBL ; European Research Council ; Max Planck Society ; NIGMS U01 GM110749; Royal Society of New Zealand Marsden award ; Swiss National Science foundation |
PMID:30958812 | Free, Available for download, Freely available | SCR_017307 | , Beast 2.5 | 2026-09-05 06:28:22 | 211 | |||||||
|
SequelQC Resource Report Resource Website 1+ mentions |
SequelQC (RRID:SCR_017279) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data. | raw, data, PacBio, Sequel, analysis, sequence, DNA, read, length, plot | NSF Plant Genome Research Program IOS-1744001 | DOI:10.1101/611814 | Free, Freely available, Available for download | SCR_017279 | 2026-09-05 06:28:21 | 2 | |||||||||
|
GeneMarkS-T Resource Report Resource Website 100+ mentions |
GeneMarkS-T (RRID:SCR_017648) | data analysis software, data processing software, software application, software resource | Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark. | Identification, protein, coding, region, RNA, transcript, gene, discovery, eukaryotic, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Georgia Institute of Technology; Georgia; USA |
NHGRI HG000783 | PMID:25870408 | Restricted | biotools:GeneMarkS-t | https://bio.tools/GeneMarkS-T | SCR_017648 | 2026-09-05 06:28:27 | 172 | ||||||
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Canadian Epigenetics, Environment and Health Research Consortium Network Resource Report Resource Website |
Canadian Epigenetics, Environment and Health Research Consortium Network (RRID:SCR_017491) | consortium, data or information resource, organization portal, portal | Network to connect Canadian epigenetics researchers and expand their reach to broader health research community in Canada and beyond. Curated epigenomics sequence focused on common human diseases. | Curated, epigenomic, sequence, human, disease | is related to: International Human Epigenome Consortium | Canadian Institutes of Health Research (CIHR) ; Genome Canada |
Free, Freely available | SCR_017491 | CEEHRC Network | 2026-09-05 06:28:25 | 0 | ||||||||
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RAMPAGE Resource Report Resource Website 100+ mentions |
RAMPAGE (RRID:SCR_017590) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2021.Web based structural analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB. Used to visualize dihedral angles ψ against φ of amino acid residues in protein structure. | Ramachandran, plot, analysis, upload, PDB, file, coputing, dihedral, angle, extracting, sequence, protein, amino acid, residue, structure | has parent organization: University of Cambridge; Cambridge; United Kingdom | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_017590 | 2026-09-05 06:28:26 | 136 | ||||||||||
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AmoebaDB Resource Report Resource Website 1+ mentions |
AmoebaDB (RRID:SCR_017592) | analysis service resource, data or information resource, database, production service resource, service resource | Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers. | Genomic, functional, database, Entamoeba, Acanthamoeba, parasite, microarray, expression, data, experimental, isolate, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Eukaryotic Pathogen Database Resources |
Department of Health and Human Services ; NIDA ; NIH |
PMID:20974635 | Free, Freely available | biotools:amoebadb, r3d100012457 | https://bio.tools/amoebadb, https://doi.org/10.17616/R3PX9Q | SCR_017592 | 2026-09-05 06:28:26 | 8 | ||||||
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Michigan Imputation Server Resource Report Resource Website 100+ mentions |
Michigan Imputation Server (RRID:SCR_017579) | data access protocol, service resource, software resource, web service | Web server to implement whole genotype imputation workflow for efficient parallelization of computationally intensive tasks. Service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity. Used to find haplotype segments and reference panel of sequenced genomes, assign genotypes at untyped markers, improve genome coverage, facilitate comparison and combination of studies that use different marker panels, increase power to detect genetic association, and guide fine mapping. | Whole, genotype, imputation, workflow, parallelization, task, find, haplotype, segment, reference, panel, sequence, genome, mapping | has parent organization: University of Michigan; Ann Arbor; USA | Austrian Science Fund ; European Community Seventh Framework Programme ; NHGRI HG000376; NHGRI HG007022; NHLBI HL117626; NIA ; NIDA R01 DA037904 |
PMID:27571263 | Restricted | https://github.com/genepi/imputationserver | SCR_017579 | Next Generation Genotype Imputation Service | 2026-09-05 06:28:26 | 196 | ||||||
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Bowtie 2 Resource Report Resource Website 1000+ mentions |
Bowtie 2 (RRID:SCR_016368) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | 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 | 2026-09-05 06:27:50 | 1993 | |||||
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Hypermut Resource Report Resource Website 100+ mentions |
Hypermut (RRID:SCR_014933) | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Web application for the analysis and detection of APOBEC-induced hypermutations. The first sequence in the input alignment will be used as the reference sequence, and each of the other sequences will be used as a query sequence. | mutation, hypermutation, sequence, sequence analysis software genome, web application | PMID:10869039 | SCR_014933 | Hypermut 2.0 | 2026-09-05 06:27:52 | 130 |
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