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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | software toolkit, software resource, software application, data management software, data analysis software, data processing software | 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 | 2026-08-08 12:00:45 | 344 | ||||||
|
ALTER Resource Report Resource Website 100+ mentions |
ALTER (RRID:SCR_015968) | web application, sequence analysis software, image analysis software, software resource, software application, data analysis software, alignment software, data processing software | 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 | 2026-08-08 12:00:27 | 125 | |||||
|
AMAP Resource Report Resource Website 100+ mentions |
AMAP (RRID:SCR_015969) | image analysis software, software resource, software application, source code, alignment software, 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 | 2026-08-08 12:00:45 | 400 | ||||
|
Aragorn Resource Report Resource Website 100+ mentions |
Aragorn (RRID:SCR_015974) | sequence analysis software, software resource, software application, data 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 | 2026-08-08 12:00:46 | 474 | |||||||
|
Arden Resource Report Resource Website 10+ mentions |
Arden (RRID:SCR_015975) | software toolkit, image analysis software, software resource, software application, source code, alignment software, data processing software | 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 | 2026-08-08 12:00:27 | 49 | |||||
|
DIAMOND Resource Report Resource Website 100+ mentions |
DIAMOND (RRID:SCR_016071) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search. | sequence, aligner, high, performance, analysis, big, data, protein, DNA, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
PMID:25402007 DOI:10.1038/nmeth.3176 |
Free, Available for download | OMICS_08011, biotools:diamond | https://bio.tools/diamond, https://sources.debian.org/src/diamond-aligner/ | SCR_016071 | 2026-08-08 12:00:48 | 489 | |||||||
|
Circlator Resource Report Resource Website 100+ mentions |
Circlator (RRID:SCR_016058) | software toolkit, image analysis software, software resource, software application, alignment software, data processing software | Software that automates assembly circularization and produces accurate linear representations of circular sequences. It is used for assembling of DNA sequence data of complete bacterial and small eukaryotic genomes. | assembly, sequence, genome, DNA, circularization, accurate, bacteria, erukaryote, tool |
is listed by: Debian is listed by: OMICtools |
Wellcome Trust grant 098051 | PMID:26714481 DOI:10.1186/s13059-015-0849-0 |
Free, Available for download | OMICS_09488 | https://github.com/sanger-pathogens/circlator, https://sources.debian.org/src/circlator/ | SCR_016058 | 2026-08-08 12:00:28 | 363 | ||||||
|
Clearcut Resource Report Resource Website 10+ mentions |
Clearcut (RRID:SCR_016059) | software resource, software application, standalone software, data visualization software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023.Software as a stand-alone reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm. Used in distance-based phylogenetic tree reconstruction method to process large sequence datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rnj, phylogenetic, tree, construction, neighbor, joining, distance, method, reference, standalone, implemetation, relaxed, algorithm, phylogenetic, tree, reconstruction, sequence |
is listed by: Debian is listed by: OMICtools is related to: University of Idaho; Idaho; USA |
NIH P20 RR16448; INBRE Program of the National Center for Research Resources ; NSF EPS 00809035; NIH P20 RR16454 |
PMID:16752216 DOI:10.1007/s00239-005-0176-2 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15083 | https://github.com/ibest/clearcut, https://sources.debian.org/src/clearcut/ | SCR_016059 | 2026-08-08 12:00:47 | 26 | ||||||
|
Nanopolish Resource Report Resource Website 100+ mentions |
Nanopolish (RRID:SCR_016157) | software resource, software application, data analysis software, data processing software | Software package for signal-level analysis of Oxford Nanopore sequencing data. | Signal level analysis, Oxford Nanopore, sequencing data, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_16545, biotools:nanopolish | https://bio.tools/nanopolish, https://sources.debian.org/src/nanopolish/ | SCR_016157 | 2026-08-08 12:00:29 | 477 | ||||||||
|
HiLive Resource Report Resource Website |
HiLive (RRID:SCR_016134) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software tool for performing read mapping that maps Illumina HiSeq sequencer read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications. | perform, read, mapping, sequence, alignment, analysis, Illumina, time, critical, clinical, application |
is listed by: Debian is listed by: OMICtools |
the German Federal Ministry of Health IIA5-2512-FSB-725 | PMID:27794555 | Free, Available for download | OMICS_13393 | https://sources.debian.org/src/hilive/ | https://sourceforge.net/projects/hilive/ | SCR_016134 | 2026-08-08 12:00:29 | 0 | |||||
|
FSA Resource Report Resource Website 1+ mentions |
FSA (RRID:SCR_016114) | FSA | image analysis software, software resource, software application, alignment software, data processing software | Software for a statistical multiple sequence alignment algorithm which uses a "distance-based" approach to align homologous protein, RNA or DNA sequences. The GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned. | multiple, sequence, alignment, algorithm, distance, approach, homologous, protein, DNA, RNA, acurate, fast |
is listed by: Debian is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
PMID:19478997 | Free, available for download | https://sources.debian.org/src/fsa/ | SCR_016114 | Fast Statistical Alignment, FSA: Fast Statistical Alignment | 2026-08-08 12:00:28 | 3 | ||||||
|
GARLI Resource Report Resource Website 100+ mentions |
GARLI (RRID:SCR_016117) | GARLI | software resource, software application, data analysis software, data processing software | Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution. | inference, phylogenetic, tree, analysis, molecular, sequence, data, maximum, likelihood, criterion, nucleotide, amino acid, codon, model, evolution |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_04234 | https://code.google.com/archive/p/garli/, https://sources.debian.org/src/garli/ | SCR_016117 | Genetic Algorithm for Rapid Likelihood Inference | 2026-08-08 12:00:28 | 280 | ||||||
|
Fsm-lite Resource Report Resource Website 10+ mentions |
Fsm-lite (RRID:SCR_016115) | software resource, software application, data analysis software, data processing software | Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data. | protein, dna, rna, sequence, analysis, core, implementation, frequency, based, substring, mining, extract, discriminate, dataset, sequencing, high throughput |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_28406 | https://sources.debian.org/src/fsm-lite/ | SCR_016115 | fsm, Frequency-based String Mining, Frequency-based String Mining (lite) | 2026-08-08 12:00:48 | 19 | |||||||
|
gdpc Resource Report Resource Website |
gdpc (RRID:SCR_016119) | software resource, software application, data visualization software, data processing software | Software application for visualizing output data from molecular dynamics simulations. It can be customized to read almost any input file format, animate it, and output images of each frame. | visualizing, output, data, molecular, dynamic, simulation, animation, visualization |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_19946 | https://sources.debian.org/src/gdpc/ | http://www.frantz.fi/software/gdpc.php, https://directory.fsf.org/wiki/Gdpc | SCR_016119 | 2026-08-08 12:00:49 | 0 | |||||||
|
Edtsurf Resource Report Resource Website 1+ mentions |
Edtsurf (RRID:SCR_016083) | software resource, software application, source code, data visualization software, data processing software | Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening. | construct, triangulate, surface, macromolecule, van der Waals, solvent, accessible, molecular, cavities, program |
is listed by: Debian is listed by: OMICtools |
the Alfred P. Sloan Foundation ; NIGMS GM083107; NIGMS GM084222; NSF 0746198 |
PMID:19956577 | Free, Available for download, Freely available | OMICS_16795 | https://sources.debian.org/src/edtsurf/ | SCR_016083 | EDTSurf: Quick and accurate construction of macromolecular surfaces | 2026-08-08 12:00:28 | 4 | |||||
|
E-mem Resource Report Resource Website 10+ mentions |
E-mem (RRID:SCR_016081) | E-mem | image analysis software, software resource, software application, standalone software, alignment software, data processing software | Software for an efficient maximal exact match (MEM) computation program that does not use full text indexes, uses less space and is amenable to parallelization. It can be used as a stand alone application or a drop-in replacement for MUMmer3 system for rapidly aligning entire genomes. | efficient, maximal, exact, match, compute, program, algorithm, application, sequence, alignment |
is listed by: Debian is listed by: OMICtools has parent organization: Department of Computer Science; University of Western Ontario; London; Ontario; Canada |
Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant R3143A01 (L.I.). | PMID:25399029 | Free, Available for download | OMICS_08451 | https://github.com/lucian-ilie/E-MEM, https://sources.debian.org/src/e-mem/ | SCR_016081 | E-mem: Efficient-maximal exact match | 2026-08-08 12:00:48 | 12 | ||||
|
GenomeTools Resource Report Resource Website 100+ mentions |
GenomeTools (RRID:SCR_016120) | sequence analysis software, software toolkit, software resource, software application, data analysis software, data processing software | Software toolkit for biological sequence analysis and -presentation combined into a single binary. It is used for genome analysis, efficient processing of structured genome annotations and contains binaries for sequence and annotation handling, sequence compression, index structure generation and access, annotation visualization. | analysis, genome, annotate, sequence, compress, visualization, single, binary, combine, structure, efficient |
is listed by: Debian is listed by: OMICtools |
PMID:24091398 | Free, Available for download | OMICS_16119 | https://sources.debian.org/src/genometools/ | SCR_016120 | GenomeTool, Genome Tools, Genome Tool | 2026-08-08 12:00:28 | 150 | ||||||
|
bioSyntax Resource Report Resource Website 1+ mentions |
bioSyntax (RRID:SCR_016207) | data management software, software resource, software application | Software for syntax highlighting for computational biology. | computation, syntax, language, code, scientific, data, workflow, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
DOI:10.1186/s12859-018-2315-y | Free, Available for download | biotools:biosyntax, OMICS_25594 | https://github.com/bioSyntax/bioSyntax, https://bio.tools/biosyntax, https://sources.debian.org/src/biosyntax/ | SCR_016207 | 2026-08-08 12:00:50 | 2 | |||||||
|
lilikoi Resource Report Resource Website 1+ mentions |
lilikoi (RRID:SCR_016361) | software toolkit, software resource, software application, data analysis software, data processing software | Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction. | personalized, medicine, metabolomics, data, classification, clustering, biomarker, prediction, algorithm, calculating, microarray, enrichment |
is listed by: OMICtools is related to: University of Hawaii; Hawaii; USA |
NIEHS K01 ES025434; NIGMS GM103457; NLM R01 LM012373; NICHD R01 HD084633 |
DOI:https://doi.org/10.1101/283408 | Free, Available for download, Freely available | https://omictools.com/lilikoi-tool | SCR_016361 | 2026-08-08 12:00:30 | 3 | |||||||
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AbundantOTU+ Resource Report Resource Website 1+ mentions |
AbundantOTU+ (RRID:SCR_016527) | AbundantOTU | sequence analysis software, software resource, software application, data analysis software, data processing software | Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset. | pyrosequencing, 16S, rRNA, gene, operational, taxonomic, unit, abundant, species, dataset |
is listed by: OMICtools has parent organization: Indiana University; Indiana; USA |
NHGRI R01 HG004908; NHLBI U01 HL09896001 |
PMID:22102981 | Free, Available for download, Freely available | SCR_016527 | AbundantOTU:Abundant Operational Taxonomic Unit, Abundant OTU, AbundantOTU+ | 2026-08-08 12:00:32 | 1 |
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