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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
jModelTest Resource Report Resource Website 1000+ mentions |
jModelTest (RRID:SCR_015244) | data analysis software, source code, software application, software resource, data processing software | Software tool used to carry out statistical selection of best-fit models of nucleotide substitution without the aid of PAUP*. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests, Akaike and Bayesian information criteria, and a decision theory method. It also provides estimates of model selection uncertainty, parameter importances, and model-averaged parameter estimates. | best-fit model, nucleotide substitution, statistical analysis |
is listed by: Debian is listed by: OMICtools |
DOI:10.1038/nmeth.2109 | Available for download | OMICS_11546 | https://sources.debian.org/src/jmodeltest/ | SCR_015244 | 2026-07-31 09:27:45 | 3726 | |||||||
|
GEN3VA Resource Report Resource Website 1+ mentions |
GEN3VA (RRID:SCR_015682) | data processing software, data analysis software, software application, software resource | 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 | 2026-07-31 09:27:44 | 5 | |||||
|
BCBtoolkit Resource Report Resource Website 50+ mentions |
BCBtoolkit (RRID:SCR_015519) | software toolkit, data analysis software, software application, software resource, data processing software | 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 | 2026-07-31 09:27:49 | 58 | |||||||
|
Ariba Resource Report Resource Website 100+ mentions |
Ariba (RRID:SCR_015976) | software toolkit, data analysis software, software application, software resource, sequence analysis software, data processing software | Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling. | software, analysis, tool, sequence, antibiotic, resistance, assembly, local, mlst |
is listed by: Debian is listed by: OMICtools |
Wellcome Trust 206194; Biotechnology and Biological Sciences Research Council BB/M014088/1 |
PMID:29177089 DOI:10.1099/mgen.0.000131 |
Free, Available for download, Freely available | OMICS_17327 | https://sources.debian.org/src/artemis/ | SCR_015976 | 2026-07-31 09:27:54 | 197 | ||||||
|
Atac Resource Report Resource Website 1000+ mentions |
Atac (RRID:SCR_015980) | image analysis software, data analysis software, alignment software, software application, software resource, sequence analysis software, data processing software | 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 | 2026-07-31 09:27:54 | 1748 | |||||||
|
BALLView Resource Report Resource Website 1+ mentions |
BALLView (RRID:SCR_015986) | data visualization software, software application, data processing software, software resource, standalone software, simulation software | Software for molecular visualization and modeling. It provides fast OpenGL-based visualization of molecular structures, molecular mechanics methods (minimization, MD simulation using the AMBER, CHARMM, and MMFF94 force fields), calculation and visualization of electrostatic properties (FDPB) and molecular editing features. | molecular, modeling, visualization, application, computation, algorithm, library, bioinformatics |
is listed by: Debian is listed by: OMICtools |
Deutsche Forschungsgemeinschaft BIZ 1/1-3; BIZ 4/1-1 and LE 952/2-3 |
PMID:16332707 DOI:10.1093/bioinformatics/bti818 |
Free, Freely available, Free for download, Runs on Mac OS, Runs on Windows | OMICS_05049 | https://github.com/BALL-Project/ball/wiki/Tutorials, https://sources.debian.org/src/bamtools/ | SCR_015986 | BALL:Biochemical Algorithms Library, Biochemical Algorithms Library | 2026-07-31 09:27:54 | 4 | |||||
|
Axe Resource Report Resource Website 1+ mentions |
Axe (RRID:SCR_015984) | software toolkit, data analysis software, software application, software resource, sequence analysis software, data processing software | Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples. | software, tool, sequence, analysis, barcode, demultiplexing |
is listed by: Debian is listed by: OMICtools |
Free, Freely available, Available for download | OMICS_19788 | https://readthedocs.org/projects/axe-demultiplexer/, https://sources.debian.org/src/baitfisher/ | SCR_015984 | Axe-demultiplexer | 2026-07-31 09:27:55 | 1 | |||||||
|
Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | software toolkit, data analysis software, data management software, software application, data processing software, software resource | 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 | 2026-07-31 09:27:55 | 324 | ||||||
|
scater Resource Report Resource Website 100+ mentions |
scater (RRID:SCR_015954) | data visualization software, software toolkit, data analysis software, software application, software resource, sequence analysis software, data processing software | 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) | 2026-07-31 09:27:48 | 173 | ||||||
|
ALTER Resource Report Resource Website 100+ mentions |
ALTER (RRID:SCR_015968) | image analysis software, data analysis software, web application, alignment software, software application, data processing software, sequence analysis software, software resource | 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 | 2026-07-31 09:27:54 | 112 | |||||
|
AMAP Resource Report Resource Website 100+ mentions |
AMAP (RRID:SCR_015969) | image analysis software, alignment software, source code, software application, software resource, data processing software | Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method. | software, peptide, sequence, alignment, annealing, bioinformatics, multiple, svn, posterior, decoding |
is listed by: Debian is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
NSF EF 03-31494; NHGRI R01 HG2362; NSF CCF0347992 |
PMID:17237099 DOI:10.1093/bioinformatics/btl311 |
Free, Available for download | OMICS_19787 | http://baboon.math.berkeley.edu/amap/, https://sources.debian.org/src/amap-align/ | https://sources.debian.org/src/amos-assembler/ | SCR_015969 | amap-align | 2026-07-31 09:27:54 | 388 | ||||
|
Aragorn Resource Report Resource Website 100+ mentions |
Aragorn (RRID:SCR_015974) | data analysis software, software application, software resource, sequence analysis software, data processing software | Software that detects tRNA genes and tmRNA genes in nucleotide sequences. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base‐paired cloverleaf., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | software, program, nucleotide, sequence, detect, tmRNA, tRNA |
is listed by: Debian is listed by: OMICtools |
PMID:14704338 DOI:10.1093/nar/gkh152 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04227 | https://sources.debian.org/src/arden/ | SCR_015974 | 2026-07-31 09:27:48 | 472 | |||||||
|
Arden Resource Report Resource Website 10+ mentions |
Arden (RRID:SCR_015975) | image analysis software, software toolkit, alignment software, source code, software application, data processing software, software resource | Software for specificity control of read alignments using an artificial reference. It estimates error rates based on real experimental reads and an additionally generated artificial reference genome. It can be used to optimize parameters for read mappers, to select read mappers for a specific problem or also to filter alignments based on quality estimation. | software, alignment, artificial, reference, estimate, error, genome, false, positive, next, generation, sequencing, DNA, python |
is listed by: Debian is listed by: OMICtools |
Robert Koch-Institute (RKI) | PMID:23685787 DOI:10.1093/bioinformatics/btt255 |
Free, Freely available | OMICS_09783 | https://sources.debian.org/src/ariba/ | SCR_015975 | ARDEN: Artificial Reference Driven Estimation of false positives in NGS data, Artificial Reference Driven Estimation of false positives in NGS data | 2026-07-31 09:27:54 | 48 | |||||
|
LoRDEC Resource Report Resource Website 100+ mentions |
LoRDEC (RRID:SCR_015814) | data analysis software, software application, software resource, sequence analysis software, data processing software | Software that performs hybrid error correction for long, PacBio reads. LoRDEC can correct insertions, deletions, and substitutions in PacBio reads. | hybrid error correction, pacbio read, long error correction, real-time sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools |
Academy of Finland 267591; ANR Colib’read ANR-12-BS02-0008 |
PMID:25165095 | Free, Available for download | biotools:lordec | https://bio.tools/lordec | SCR_015814 | 2026-07-31 09:27:54 | 206 | ||||||
|
UALCAN Resource Report Resource Website 1000+ mentions |
UALCAN (RRID:SCR_015827) | data or information resource, data analysis software, database, web application, software application, software resource, sequence analysis software, data processing software | Web application and database for analyzing cancer transcriptome data. It also has applications is facilitating tumor subgroup gene expression and survival analyses. | tumor, gene expression, survival analysis, cancer transcriptome data, sequencing, biomarker, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:28732212 | Freely available | biotools:UALCAN | https://bio.tools/UALCAN | SCR_015827 | 2026-07-31 09:27:54 | 2853 | |||||||
|
circlncRNAnet Resource Report Resource Website 10+ mentions |
circlncRNAnet (RRID:SCR_015794) | data or information resource, database, web application, data processing resource, software resource | Web application for mapping functional networks of long or circular forms of non-coding RNAs. It supports the uploading and processing of user-defined NGS-based gene expression matrix data. | mapping, long form, circular form, non-coding rna, rna mapping, regulatory rna, ncRNA, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian requires: RStudio |
Freely available, Free, Available for download, Runs on Linux, Demo available, Tutorial available | biotools:circlncrnanet | https://github.com/smw1414/circlncRNAnet, https://bio.tools/circlncrnanet | SCR_015794 | 2026-07-31 09:27:52 | 31 | ||||||||
|
VaDiR Resource Report Resource Website 10+ mentions |
VaDiR (RRID:SCR_015797) | VaDiR | data analysis software, software application, data processing software, sequence analysis software, software resource, algorithm resource | Method for uncovering mutations from RNA sequencing datasets that could be useful in further functional analysis. It also allows orthogonal validation of DNA-based mutation discovery by providing complementary sequence variation analysis from paired RNA/DNA sequencing data sets. | rna-seq, somatic variant calling, ovarian cancer, cancer genomes transcriptome, orthogonal validation, genetic mutation, sequence variation analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
NCI P30 CA168524; Department of Defense Ovarian Cancer Research Program W81XWH-10-1-0386; University of Kansas Endowment Association ; Biostatistics and Informatics Shared Resource (BISR) ; Cancer Center Cancer Biology program |
DOI:10.5524/100360 | Free, Available for download | biotools:vadir | ftp://penguin.genomics.cn/pub/10.5524/100001_101000/100360/, https://bio.tools/vadir | SCR_015797 | VaDiR: an integrated approach to Variant Detection in RNA | 2026-07-31 09:27:52 | 13 | ||||
|
Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | software toolkit, data analysis software, software application, software resource, sequence analysis software, data processing software | Software toolkit for analyzing nanopore sequence data. | nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Medical Research Council ; NHGRI R01 HG006693 |
PMID:25143291 | Open source, Free, Available for download | biotools:poretools | https://bio.tools/poretools | SCR_015879 | 2026-07-31 09:27:54 | 81 | ||||||
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SwissTree Resource Report Resource Website 1+ mentions |
SwissTree (RRID:SCR_015881) | project portal, data or information resource, data repository, storage service resource, portal, service resource, data set | Project that aims to provide a collection of Gold Standard gene phylogenies to the scientific community. This set of reference gene trees is suitable for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure. | gene phylogeny, gene collection, gold standard, phylogenomic, database, genome analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Swiss State Secretariat for Education ; Research and Innovation (SERI) ; Swiss National Science Foundation 150654 |
Public, Free, Available for download | biotools:swisstree | https://bio.tools/swisstree | SCR_015881 | 2026-07-31 09:27:53 | 3 | |||||||
|
PhyD3 Resource Report Resource Website 10+ mentions |
PhyD3 (RRID:SCR_015892) | PhyD3 | data visualization software, web application, software application, data processing software, software resource | Web application that is a phylogenetic tree viewer based on d3.js. It was developed as an alternative to Archaeopteryx inspired by d3.phylogram.js. | javascript, visualization, toolkit, phylogeny, program, phylogenetic data, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28525531 | Open source, Demo available | biotools:phyd3 | https://github.com/vibbits/phyd3, https://bio.tools/phyd3 | SCR_015892 | 2026-07-31 09:27:54 | 47 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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