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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MITE-Tracker Resource Report Resource Website 1+ mentions |
MITE-Tracker (RRID:SCR_017030) | MITE Tracker | data analysis software, data processing software, sequence analysis software, software application, software resource | Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences. | genomic, sequence, discover, miniature, inverted, repeat, transposable, element, clustering, cdhit |
uses: NCBI BLAST is listed by: OMICtools is related to: Python Programming Language |
National Council for Science and Technology ; Argentina ; National Institute of Agricultural Technology |
DOI:10.1186/s12859-018-2376-y | Free, Available for download, Freely available | OMICS_32242 | SCR_017030 | MITE Tracker, Miniature Inverted repeats Transposable Elements Tracker | 2026-09-05 06:28:17 | 4 | |||||
|
WTDBG Resource Report Resource Website 50+ mentions |
WTDBG (RRID:SCR_017225) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time. | sequence, assembler, de novo, long, noisy, read, likelihood, estimator, genome |
is listed by: OMICtools is listed by: Debian |
NHGRI R01 HG010040; NSFC |
PMID:31819265 | Free, Available for download, Freely available | OMICS_24025 | https://github.com/ruanjue/wtdbg, https://sources.debian.org/src/wtdbg2/ | SCR_017225 | Wtdbg2, wtdgb, Wtdgb, wtdgb2 | 2026-09-05 06:28:20 | 66 | |||||
|
PSMC Resource Report Resource Website 10+ mentions |
PSMC (RRID:SCR_017229) | data analysis software, data processing software, software application, software resource | Software package for implementation of Pairwise Sequentially Markovian Coalescent model. Infers population size history from diploid sequence. | pairwise, sequentially, Markovian, coalescent, model, infer, population, size, history, diploid, sequence | Free, Available for download, Freely available | SCR_017229 | Pairwise Sequentially Markovian Coalescent | 2026-09-05 06:28:20 | 17 | ||||||||||
|
prank Resource Report Resource Website 100+ mentions |
prank (RRID:SCR_017228) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software application as probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Allows for defining potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences. | multiple, nucleotide, sequence, alignment, DNA, codon, amino acid, phylogenetic, gap, predict, location, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:24170401 PMID:21110866 |
Free, Available for download, Freely available | biotools:prank, SCR_024174, OMICS_12425 | https://www.ebi.ac.uk/goldman-srv/webprank/, https://ariloytynoja.github.io/prank-msa/, https://bio.tools/prank | https://omictools.com/prank-tool | SCR_017228 | PRANK | 2026-09-05 06:28:20 | 281 | |||||
|
matemaker Resource Report Resource Website 1+ mentions |
matemaker (RRID:SCR_017199) | data analysis software, data processing software, sequence analysis software, software application, software resource, standalone software | Software tool to make artificial mate pairs from long sequences for scaffolding. | artificial, mate, pair, long, sequence, scaffolding, genomics, genome, assembly | Free, Available for download, Freely available | SCR_017199 | matemaker v1.0.0 | 2026-09-05 06:28:20 | 4 | ||||||||||
|
Open Ephys: Pulse Pal Resource Report Resource Website 1+ mentions |
Open Ephys: Pulse Pal (RRID:SCR_017203) | instrument resource | Open source pulse train generator that allows users to create and trigger software defined trains of voltage pulses with high temporal precision. Generates precisely timed pulse sequences for use in research involving electrophysiology or psychophysics. | instrument, generator, stimulation, voltage, puls, sequence, electrophysiology, psychophysics | McKnight Foundation ; NIMH R01 MH097061; NINDS R01 NS07553 |
DOI:10.3389/fneng.2014.00043 | Available for purchase | https://sanworks.io/shop/viewproduct?productID=1102, https://github.com/sanworks/PulsePal, https://sites.google.com/site/pulsepalwiki/specifications?authuser=0 | SCR_017203 | Pulse Pal v2 | 2026-09-05 06:28:20 | 2 | |||||||
|
GraphClust2 Resource Report Resource Website 1+ mentions |
GraphClust2 (RRID:SCR_017286) | data analysis software, data processing software, software application, software resource, web application | Software tool for scalable clustering of RNAs based on sequence and secondary structures similarities. Implemented within Galaxy framework. Used for studying RNA function. | scalable, clustering, RNA, sequence, secondary, structure, function, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
German Federal Ministry of Education and Research ; German Research Foundation Collaborative Research Centre 992 Medical Epigenetics |
PMID:31808801 PMID:22689765 |
Free, Available for download, Freely available | biotools:GraphClust2 | https://bio.tools/GraphClust2 | SCR_017286 | GraphClust, GraphClust-2 | 2026-09-05 06:28:22 | 4 | |||||
|
PILER Resource Report Resource Website 10+ mentions |
PILER (RRID:SCR_017333) | data analysis software, data processing software, software application, software resource | Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats. | analysis, repetitive, DNA, genome, sequence, classification, alignment | is listed by: OMICtools | PMID:15961452 | Free, Available for download, Freely available | https://omictools.com/piler-tool | SCR_017333 | 2026-09-05 06:28:22 | 15 | ||||||||
|
Webcutter Resource Report Resource Website 10+ mentions |
Webcutter (RRID:SCR_017638) | analysis service resource, data access protocol, data analysis service, data analysis software, data processing software, production service resource, sequence analysis software, service resource, software application, software resource, web service | Software tool to find restriction endonucleases. Helps restriction map nucleotide sequences. Tool with customizable interface, platform independent accessibility, interfaces to NCBI's GenBank, DNA sequence database, and NEB's REBase, and restriction enzyme database. In addition to restriction site mapping, Webcutter 2 also performs degenerate digests, including option of finding restriction sites that can be introduced into sequence by silent mutagenesis. | Find, restriction, site, endonuclease, map, nucleotide, DNA, sequence, degenarte, digest, silent, mutagenesis |
has parent organization: Yale University; Connecticut; USA works with: GenBank works with: REBASE |
Free, Freely available | SCR_017638 | Webcutter 2.0, Webcutter 2 | 2026-09-05 06:28:27 | 15 | |||||||||
|
refgenie Resource Report Resource Website 1+ mentions |
refgenie (RRID:SCR_017574) | data management software, service resource, software application, software resource | Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis. | Organize, retrive, share, genome, analysis, reference, assembly, asset, manager, sequence, annotation, file, command, line, interface, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/698704 | Free, Available for download, Freely available | biotools:Refgenie | https://bio.tools/Refgenie | SCR_017574 | reference genome manager | 2026-09-05 06:28:26 | 7 | ||||||
|
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 | 2026-09-05 06:28:02 | 5 | ||||||
|
Belvu Resource Report Resource Website 10+ mentions |
Belvu (RRID:SCR_015989) | alignment software, data processing software, image analysis software, software application, software resource | Software for multiple sequence alignment viewing, editing and phylogeny. It includes a set of user-configurable modes to color residues used to create high-quality reference alignments. | editing, phylogeny, sequence, alignment, phylogenetic, viewer, multiple, editor, color, residue, reference |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
NHGRI U54 HG00455; Wellcome Trust Grant 098051 |
PMID:26801397 | Free, Available for download | SCR_015989 | 2026-09-05 06:28:02 | 18 | ||||||||
|
Aevol Resource Report Resource Website 1+ mentions |
Aevol (RRID:SCR_015966) | simulation software, software application, software resource | Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences). | software, genetic, model, simulation, evolution, microorganism, coding, sequence, algorithm | Agence Nationale de la Recherche ANR-10-BLAN-1724; INSERM |
PMID:24278000 | Free, Available for download, Tutorial available | SCR_015966 | 2026-09-05 06:28:01 | 3 | |||||||||
|
Anfo Resource Report Resource Website 1+ mentions |
Anfo (RRID:SCR_015972) | alignment software, data processing software, image analysis software, software application, software resource | Software for short read alignment and mapping of sequencing reads where the DNA sequence is somehow modified and/or there is more divergence between sample and reference than what fast mappers will handle. | alignment, program, mapper, software, sequence, DNA, ancient dna, bisulphite, treatment | Free Software Foundation ; Inc. |
Free, Available for download, Freely available | SCR_015973 | SCR_015972 | Anfo Short Read Aligner/Mapper | 2026-09-05 06:28:01 | 8 | ||||||||
|
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 | 2026-09-05 06:28:03 | 71 | ||||
|
Dotter Resource Report Resource Website 50+ mentions |
Dotter (RRID:SCR_016080) | alignment software, data analysis software, data processing software, data visualization software, image analysis software, sequence analysis software, software application, software resource | Software for sequence alignment that is a graphical dot-matrix program for detailed comparison of two sequences. | sequence, alignment, graphical, dot-matrix, program, comparison, two, detail |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
NHGRI U54 HG00455; Wellcome Trust Grant 098051 |
PMID:26801397 | Free, Available for download | SCR_016080 | Seqtools Dotter | 2026-09-05 06:28:03 | 84 | |||||||
|
Exonerate Resource Report Resource Website 100+ mentions |
Exonerate (RRID:SCR_016088) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, alignment, pairwise, comparison, dynamic, programming, heuristic, bio.tools |
is used by: ExonerateTransferAnnotation is listed by: Debian is listed by: bio.tools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:15713233 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:exonerate | https://bio.tools/exonerate | SCR_016088 | 2026-09-05 06:28:03 | 376 | |||||||
|
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 | 2026-09-05 06:28:03 | 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 | 2026-09-05 06:28:03 | 0 | |||||
|
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 | 2026-09-05 06:28:03 | 407 |
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