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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GensearchNGS Resource Report Resource Website 10+ mentions |
GensearchNGS (RRID:SCR_010802) | GensearchNGS | software resource | An integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Roche/454, Illumina and Ion Torrent. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Commercial license | OMICS_00287, biotools:gensearchngs | https://bio.tools/gensearchngs | SCR_010802 | 2026-09-19 12:52:00 | 23 | |||||||
|
AgileVariantMapper Resource Report Resource Website 1+ mentions |
AgileVariantMapper (RRID:SCR_010770) | AgileVariantMapper | software resource | Software that visualises sequence variant data from whole exome data, so that it is possible to identify autozygous regions in consanguineous individuals. | is listed by: OMICtools | PMID:23090942 | OMICS_00122 | SCR_010770 | AgileVariantMapper - Autozygosity mapping using Next generation sequence data | 2026-09-19 12:51:59 | 1 | ||||||||
|
Bustools Resource Report Resource Website 10+ mentions |
Bustools (RRID:SCR_018210) | data analysis software, data processing software, software application, software resource | Software tool for manipulating BUS files for single cell RNA-Seq datasets. Used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. | Single cell RNAseq workflow, single cell RNAseq dataset, error correct barcode, collapse UMI, produce gene count, produce transcript compatibility count matrice |
is listed by: Debian is listed by: OMICtools works with: kb_python |
DOI:10.1101/673285 | Free, Available for download, Freely available | OMICS_33004 | https://sources.debian.org/src/bustools/ | SCR_018210 | 2026-09-19 12:53:48 | 19 | |||||||
|
ChromHMM Resource Report Resource Website 50+ mentions |
ChromHMM (RRID:SCR_018141) | data analysis software, data processing software, software application, software resource | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
Alfred P. Sloan Fellowship ; CAREER Award ; NHGRI RC1HG005334; NHGRI U01 HG007912; NHGRI U54 HG004570; NIEHS R01 ES024995; NIMH U01 MH105578; NSF 0905968 |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | 2026-09-19 12:53:47 | 50 | ||||||
|
Minimap2 Resource Report Resource Website 1000+ mentions |
Minimap2 (RRID:SCR_018550) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences. | Pairwise alignment, nucleotide sequence, map DNA sequence, map mRNA sequence, reference database, spliced nucleotide sequence, bio.tools, FASEB list |
is used by: D-GENIES is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG010040 | PMID:29750242 | Free, Available for download, Freely available | OMICS_31658, biotools:minimap2 | https://bio.tools/minimap2, https://sources.debian.org/src/libminimap2-dev/ | SCR_018550 | 2026-09-19 12:53:53 | 1593 | ||||||
|
Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | data analysis software, data processing software, software application, software resource | Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. | Data matrice analysis, data matrice modification, phyloinformatics, phylogenetic tree, alignment, molecular data manipulation, data analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: NCBI |
NSF Cyberinfrastructure for Phylogenetic Research EF 0331654 | PMID:18227120 | Free, Freely available | OMICS_21687 | https://sources.debian.org/src/phyutility/ | SCR_018545 | 2026-09-19 12:53:53 | 46 | ||||||
|
Canu Resource Report Resource Website 1000+ mentions |
Canu (RRID:SCR_015880) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Canu is a fork of the Celera Assembler and is designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). | long-read, assembly, k-mer, weighting, repeat separation, adaptive, pacbio, single-molecule, sequencing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Celera assembler |
National Human Genome Research Institute ; National Science Foundation NSF IOS-1237993; US Department of Homeland Security (DHS) HSHQDC-07-C-00020 |
PMID:28298431 DOI:10.1101/071282 |
Free, Available for download | OMICS_14592, biotools:canu | http://canu.readthedocs.io/en/latest/, https://bio.tools/canu, https://sources.debian.org/src/canu/ | SCR_015880 | 2026-09-19 12:53:14 | 2451 | ||||||
|
Baitfisher Resource Report Resource Website 1+ mentions |
Baitfisher (RRID:SCR_015985) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments. | software, package, multispecies, comparative, genomics, hybrid, enrichment, DNA, probe, design, sequence, alignments |
is listed by: Debian is listed by: OMICtools |
German Research Foundation (DFG) OH81/9-1; NI 1387/1-1; Spanish Ministry of Science and Education (MEC) RYC-2014-15615 |
PMID:27009209 DOI:10.1093/molbev/msw056 |
Free, Available for download | OMICS_11740 | https://sources.debian.org/src/ballview/ | SCR_015985 | 2026-09-19 12:53:15 | 5 | ||||||
|
Avogadro Resource Report Resource Website 1000+ mentions |
Avogadro (RRID:SCR_015983) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | semantic, optimization, crystallography, chemical, editor, visualization, analysis, molecular, modeling, drug, design, biomolecule, simulation, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Engineering Research Development Center W912HZ-11-P-0019; NSF DMR-1005413 |
PMID:22889332 DOI:10.1186/1758-2946-4-17 |
Open source, Free, Free to download | OMICS_04967, biotools:avogadro | http://avogadro.openmolecules.net/, https://github.com/avogadro, https://bio.tools/avogadro, https://sources.debian.org/src/axe-demultiplexer/ | SCR_015983 | 2026-09-19 12:53:15 | 2237 | ||||||
|
Bio-tradis Resource Report Resource Website 50+ mentions |
Bio-tradis (RRID:SCR_015993) | TraDIS:Transposon Directed Insertion Sequencing | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. | software, tool, analysis, data, sequencing, insertion, transponson, direct, mutant, library, perl, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Alexander von Humboldt Stiftung/Foundation ; Medical Research Council G1100100/1; Wellcome Trust WT098051 |
PMID:26794317 DOI:10.1093/bioinformatics/btw022 |
Free, Available for download, Freely available | OMICS_11083, biotools:bio-tradis | https://bio.tools/bio-tradis, https://sources.debian.org/src/bio-tradis/ | SCR_015993 | 2026-09-19 12:53:15 | 56 | |||||
|
Barrnap Resource Report Resource Website 500+ mentions |
Barrnap (RRID:SCR_015995) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multithreading, fasta, sequencing, software, predict, location, ribosomal, gene, genome, RNA, prediction, bacteria, archaea, mitochondria, eukaryote, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:barrnap, OMICS_13988 | https://github.com/tseemann/barrnap, https://bio.tools/barrnap, https://sources.debian.org/src/barrnap/ | SCR_015995 | Barrnap: Basic rapid ribosomal RNA predictor | 2026-09-19 12:53:15 | 722 | |||||||
|
Aegean Resource Report Resource Website 1+ mentions |
Aegean (RRID:SCR_015965) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more. | genome, evaluation, annotation, structure, loci |
is listed by: Debian is listed by: OMICtools |
National Science Foundation 1126267 | PMID:22852583 | Free, Available for download, Freely available, | OMICS_19721 | https://github.com/BrendelGroup/AEGeAn, https://sources.debian.org/src/aegean/ | SCR_015965 | AEGeAn: analysis and evaluation of genome annotations, Aegean Toolkit | 2026-09-19 12:53:15 | 9 | |||||
|
andi Resource Report Resource Website 10+ mentions |
andi (RRID:SCR_015971) | algorithm resource, alignment software, data processing software, image analysis software, software application, software resource | Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes. | algorithm, computing, estimate, analysis, genome, alignment, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Deutsche Forschungsgemeinschaft Pf672/3-1 | PMID:25504847 | Free, Freely available, Available for download | OMICS_09287, biotools:andi | https://bio.tools/andi, https://sources.debian.org/src/andi/ | SCR_015971 | 2026-09-19 12:53:15 | 41 | ||||||
|
DISULFIND Resource Report Resource Website 50+ mentions |
DISULFIND (RRID:SCR_016072) | Disulfinder | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks. | predict, disulfide, bonding, state, cysteine, protein, sequence, genomic, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: University of Florence; Florence; Italy |
Embark Fellowship from the Irish Research Council for Science ; Engineering and Technology ; EU NoE BIOPATTERN contract no. FP6-508803; EU STREP APrIL II contract no. FP6-508861 |
PMID:16844986 DOI:10.1093/nar/gkl266 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04214, biotools:disulfind | https://bio.tools/disulfind, https://sources.debian.org/src/disulfinder/ | SCR_016072 | Cysteines Disulfide Bonding State and Connectivity Predictor | 2026-09-19 12:53:17 | 71 | ||||
|
DeepNano Resource Report Resource Website 1+ mentions |
DeepNano (RRID:SCR_016070) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for an alternative basecaller for DNA base calling in the portable Oxford Nanopore MinION sequencing device, based on deep recurrent neural networks. Used to improve base calling accuracy and reduce sequencing error rate. | DNA, basecaller, Oxford Nanopore MinON read, sequencing, device, deep, recurrent, neural, network, accuracy, reduce, error |
is listed by: Debian is listed by: OMICtools has parent organization: Comenius University; Bratislava; Slovakia |
NVIDIA Corporation ; Slovak Research and Development Agency APVV-14-0253; VEGA 1/0684/16 (BB); VEGA 1/0719/14 (TV) |
PMID:28582401 | Free, Available for download | OMICS_14561 | http://compbio.fmph.uniba.sk/deepnano/, https://sources.debian.org/src/deepnano/ | SCR_016070 | DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads, DeepNano: alternative basecaller for MinION reads | 2026-09-19 12:53:17 | 5 | |||||
|
Falcon Resource Report Resource Website 100+ mentions |
Falcon (RRID:SCR_016089) | alignment software, data processing software, image analysis software, software application, software resource | Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes. | fast, aligner, sequencing, diploid, genome, assembly, non-inbred, rearranged, heterozygous, single-molecule |
is listed by: Debian is listed by: OMICtools is related to: Howard Hughes Medical Institute |
Gordon and Betty Moore Foundation GBMF 3034; National Science Foundation DBI-1350041; National Science Foundation IOS-1237880; National Science Foundation MCB 0929402; National Science Foundation MCB 1122246; NHGRI R01 HG006677 |
PMID:27749838 | Free, Available for download, Freely available | OMICS_13514 | https://sources.debian.org/src/falcon/ | SCR_016089 | 2026-09-19 12:53:17 | 293 | ||||||
|
Cassiopee Resource Report Resource Website |
Cassiopee (RRID:SCR_016056) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity. | genomic, sequence, DNA, RNA, protein, scan, subsequence, search, match, substitution, distance, Hamming, insertion, deletion |
is listed by: Debian is listed by: OMICtools has parent organization: Durham University; Durham; England |
Free, Available for download | OMICS_19794 | https://sources.debian.org/src/cassiopee/ | SCR_016056 | cassiopee-c | 2026-09-19 12:53:16 | 0 | |||||||
|
Cdbfasta Resource Report Resource Website |
Cdbfasta (RRID:SCR_016057) | CDB | data compression software, data processing software, data transfer software, software application, software resource, software toolkit | Software tool for indexing and retrieval of nucleotide sequences from FASTA (DNA and protein sequence alignment software) record databases. It has the option to compress data records. | index, retrieval, nucleotide, sequence, fasta, database, multi file, compress, record |
is listed by: Debian is listed by: OMICtools has parent organization: Carnegie Mellon University; Pennsylvania; USA has parent organization: University of Pittsburgh; Pennsylvania; USA |
The Free Software Foundation (FSF) | Free, Available for download | OMICS_19793 | https://github.com/gpertea/cdbfasta, https://sources.debian.org/src/cdbfasta/ | SCR_016057 | Constant DataBase | 2026-09-19 12:53:16 | 0 | |||||
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Bio++ Resource Report Resource Website 50+ mentions |
Bio++ (RRID:SCR_016055) | software application, software development tool, software library, software resource, software toolkit | Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | phylogenetic, molecular evolution, genetic, program, write, tool, visualize, edit, print, data, bioinformatic, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15696, biotools:biopp | https://sources.debian.org/src/bppsuite/, https://groups.google.com/forum/#!categories/biopp-help-forum/all-questions, https://github.com/BioPP, https://bio.tools/biopp, | SCR_016055 | Bppsuite, Bppphyview, Bio++ program suite, Bio++ Phylogenetic Viewer | 2026-09-19 12:53:16 | 65 | |||||||
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Clonalframe Resource Report Resource Website 100+ mentions |
Clonalframe (RRID:SCR_016060) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. | analysis, sequence, inference, bacteria, microevolution, multilocus, clonal, sample, chromosome, homologuous, recombination, disrupted, inheritance, DNA, genome |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust | DOI:10.1534/genetics.106.063305 | Free, Available for download | OMICS_14623 | https://github.com/xavierdidelot/ClonalFrameML, https://sources.debian.org/src/clonalframe/ | SCR_016060 | ClonalFrameML | 2026-09-19 12:53:16 | 407 |
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