This page compiles a list of software for the detection, annotation, analysis, simulation and visualization of repetitive, mobile and selfish DNA and related entities.
It is maintained by Tyler A. Elliott. It was initiated with the help of Elizabeth Smikle and Miduna Rahulan, formerly at the Centre for Biodiversity Genomics at the University of Guelph. Suggestions, updates and error corrections are welcome. Please feel free to add missing tools into the table, that would help a lot!
For resources more tailored to Prokaryotes and Viruses (as well as here and here), see the linked lists.
We encourage the authors of these tools to create pages for them on TE Hub, so that they can provide more information about their work, and link it back to this table. Please find a template software sheet here.
| Tool | DOI | Alternate URL | Keywords | Status |
|---|---|---|---|---|
| 2lpiRNApred | https://doi.org/10.1080/15476286.2020.1734382 | piRNA | Present (Jan 08 2025) | |
| 2-n-way Genome Suite | https://doi.org/10.1101/gr.262261.120 | Polymorphism, Genotype, Webserver | Present (Jan 08 2025) | |
| 4-LIN | https://doi.org/10.1093/sysbio/syac082 | Web Server, Phylogeny, Eukaryotic Retrotransposon | Present (Jan 08 2025) | |
| AAARF (Assisted Automated Assembler of Repeat Families) | https://doi.org/10.1186/1471-2105-9-235 | Homology, Alignment | Present (Jan 08 2025) | |
| AgIn | https://doi.org/10.1093/bioinformatics/btw360 | PacBio, Methylation | Present (Jan 08 2025) | |
| AlbaTraDIS | https://doi.org/10.1371/journal.pcbi.1007980 | Tn-Seq, Transposon Mutagenesis | Present (Jan 08 2025) | |
| Alien_Hunter | https://doi.org/10.1093/bioinformatics/btl369 | Genomic Island, HMM | Absent (Jan 08 2025) | |
| alu-detect | https://doi.org/10.1093/nar/gkt612 | Alu, SINE, Genotype, Polymorphism, NGS/HTS, Paired-End | Present (Jan 08 2025) | |
| AluMine | https://doi.org/10.1101/588434 | Alu, SINE, Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| Alpha-CENTAURI | https://doi.org/10.1093/bioinformatics/btw101 | Satellite, Centromere, Tandem Repeat, HMM, Long-Read | Present (Jan 08 2025) | |
| AnnoSINE | https://doi.org/10.1093/plphys/kiab524 | SINE, Annotation, HMM | Present (Jan 08 2025) | |
| AnTE | https://doi.org/10.1371/journal.pgen.1004482 | Simulation, Phylogeny, Bayesian MCMC, Ancestral Reconstruction | Absent (Jan 08 2025) | |
| ANUBIS | https://doi.org/10.1093/nar/gkaa679 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism, Visualization | Present (Jan 08 2025) | |
| ARTIST | https://doi.org/10.1371/journal.pgen.1004782 | Tn-Seq, Transposon Mutagenesis, HMM | Present (Jan 08 2025) | |
| atena | http://52.71.54.154/packages/devel/bioc/html/atena.html | Pipeline, Expression, Transcription, RNA-Seq | Present (Jan 08 2025) | |
| Attacca | https://doi.org/10.1186/1471-2105-10-281 | Integron | ||
| BacAnt | https://doi.org/10.3389/fmicb.2021.649969 | Link | IS Element, Archaeal/Bacterial Transposon, Integron, AMR/Antibiotic Resistance, Annotation, Web Server | Present (Jan 08 2025) |
| Bakta | https://doi.org/10.1099/mgen.0.000685 | Link | Metagenomics, Annotation | Present (Jan 08 2025) |
| Bellerophon | https://doi.org/10.1186/1471-2105-14-s5-s6 | Structural Variation, NGS/HTS, Paired-End | ||
| binary_plus_multi_clasification.py | https://doi.org/10.7717/peerj.11456 | Classification, LTR Retrotransposon, K-mer | Present (Jan 08 2025) | |
| BLATCAT | https://doi.org/10.1155/2014/730814 | BLAT, Homology | ||
| BreakDancer | https://doi.org/10.1038/nmeth.1363 | Structural Variation, NGS/HTS, Short-Read, Paired-End, MAQ | Absent (Jan 08 2025) | |
| breseq | https://doi.org/10.1186/1471-2164-15-1039 | Structural Variation, Polymorphism, Genotype | Absent (Jan 08 2025) | |
| BSSV | https://doi.org/10.1109/EMBC.2014.6944485 | Structural Variation, Bayesian, NGS/HTS | ||
| BWtrs | https://doi.org/10.1016/j.ygeno.2010.08.001 | Simple Sequence Repeat/Microsatellite, Web Server | Absent (Jan 08 2025) | |
| CAFE (Coefficient-based Analysis of Fitness by read Enrichments) | https://doi.org/10.1093/bioinformatics/btaa1086 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (Jan 08 2025) | |
| CAULIFINDER | https://doi.org/10.1186/s13100-022-00288-w | Detection, Annotation, EVE, Plants, Virus | Present (Jan 08 2025) | |
| CAlu Alu Classifier | https://doi.org/10.1016/j.cell.2010.05.020 | Genotype, Polymorphism, Homo sapiens, Alu, SINE, Web Server | Absent (Jan 08 2025) | |
| CARP | https://doi.org/10.1371/journal.pone.0193588 | De Novo, Library Generation, Homology, Annotation | Present (Jan 08 2025) | |
| CELLO-Seq (single CELl LOng read RNA sequencing) | https://doi.org/10.1101/2020.10.02.322073 | Single Cell, RNA-Seq, Eukaryotic Transposon | Present (Jan 08 2025) | |
| Censor | https://doi.org/10.1016/S0097-8485(96)80013-1 | Annotation, Repeat Masking | Present (Jan 08 2025) | |
| CGS | https://doi.org/10.1186/1471-2164-13-245 | Horizontal Transfer, K-mer | ||
| ChimeraTE | https://doi.org/10.1093/nar/gkad671 | RNA-Seq, Expression, Transcription, Paired-End, NGS/HTS, Chimera | Present (Jan 08 2025) | |
| CIAlign | https://doi.org/10.7717/peerj.12983 | Alignment, MSA, Manual Curation | Present (Jan 08 2025) | |
| CLARI-TE | https://doi.org/10.1186/s13059-014-0546-4 | Homology, Annotation, Nested Insertion | Present (Jan 08 2025) | |
| ClassifyTE | https://doi.org/10.1093/bioinformatics/btab146 | Classification, Eukaryotic Transposon | Present (Jan 08 2025) | |
| CLIFinder | https://doi.org/10.1093/bioinformatics/btx671 | LINE1, Transcription, RNA-Seq, Expression, Chimera, NGS/HTS | Present (Jan 08 2025) | |
| CLOVE | https://doi.org/10.1186/s12859-017-1760-3 | Structural Variation | Present (Jan 08 2025) | |
| ClustAGE | https://doi.org/10.1186/s12859-018-2154-x | Comparative, BLAST, Archaea, Bacteria | Present (Jan 08 2025) | |
| collapse_RepeatMasker_annotation | https://doi.org/10.1007/978-1-0716-2380-0_21 | Annotation | Present (Jan 08 2025) | |
| COLOMBO | https://doi.org/10.1186/1471-2105-7-142 | Genomic Island, Codon Usage, HMM | Present (Jan 08 2025) | |
| CompTIS | https://doi.org/10.1128/mSphere.00031-19 | Tn-Seq, Transposon Mutagenesis, PCA | Present (Jan 08 2025) | |
| CONJscan | https://doi.org/10.1007/978-1-4939-9877-7_19 | Plasmid, ICE/Integrative and Conjugative Element | Present (Jan 08 2025) | |
| ConTExt | https://genome.cshlp.org/content/28/5/714 | Illumina, Paired-End, Homology, NGS/HTS, Polymorphism | Present (Jan 08 2025) | |
| COSEG | Subfamily Identification, Eukaryotic Transposon, Alu, SINE | Present (Jan 08 2025) | ||
| ConsensusSV | https://doi.org/10.1093/bioinformatics/btac709 | NGS/HTS, Short Read, Illumina, Structural Variation | Present (Jan 08 2025) | |
| COPLA | https://doi.org/10.1101/2020.12.15.422809 | Plasmid, Classification, Homology | Present (Jan 08 2025) | |
| CRISPRCasTyper | https://doi.org/10.1101/2020.05.15.097824 | Link | CRISPR, Classification, Annotation | Present (Jan 08 2025) |
| DANTE | Link | Homology, Library Generation | Present (Jan 08 2025) | |
| DAWG-PAWS | https://doi.org/10.1186/1746-4811-5-8 | Homology, HMM, Annotation, Gene Prediction | Present (Jan 08 2025) | |
| DarkHorse | https://doi.org/10.1186/gb-2007-8-2-r16 | Horizontal Transfer, Homology, Phylogeny | Absent (Jan 08 2025) | |
| DARTE-QM (Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring) | https://doi.org/10.1038/s42003-022-03155-9 | AMR/Antibiotic Resistance, NGS/HTS, TruSeq | Present (Jan 08 2025) | |
| DARTS (Domain-Associated RetroTransposon Search) | https://doi.org/10.1101/2021.12.03.471067 | Pipeline, Homology, Annotation, Retrotransposon | Present (Jan 08 2025) | |
| DBSCAN-SWA | https://doi.org/10.1101/2020.07.12.199018 | Prophage/Bacteriophage, Homology | Present (Jan 08 2025) | |
| DD-Detection | https://doi.org/10.1093/bioinformatics/btv621 | NGS/HTS, Illumina, Paired-End, Polymorphism | Present (Jan 08 2025) | |
| D-Genies | https://doi.org/10.7717/peerj.4958 | Dot Plot, Visualization | Present (Jan 08 2025) | |
| DeBreak | https://doi.org/10.21203/rs.3.rs-1261915/v1 | NGS/HTS, Long-Read, Structural Variation | Present (Jan 08 2025) | |
| DeepMEI | https://doi.org/10.1101/2023.03.07.531451 | NGS/HTS, Short Read, Genotype, Polymorphism, Convolutional Neural Network | Present (Jan 08 2025) | |
| DeepRepeat | https://doi.org/10.1186/s13059-022-02670-6 | NGS/HTS, Short Tandem Repeat, Long-Read, Oxford Nanopore | Present (Jan 08 2025) | |
| DeepTE | https://doi.org/10.1093/bioinformatics/btaa519 | Classification, Convolutional Neural Network | Present (Jan 08 2025) | |
| Delly | https://doi.org/10.1093/bioinformatics/bts378 | Structural Variation, NGS/HTS, Short-Read, Paired-End | Present (Jan 08 2025) | |
| de_novo-identification | https://doi.org/10.13140/RG.2.2.27068.69765 | De Novo, Eukaryotic Transposon | Present (Jan 08 2025) | |
| DEPht | https://doi.org/10.1093/nar/gkac273 | Annotation, Extraction, Prophage/Bacteriophage | Present (Jan 08 2025) | |
| DeRIP | https://doi.org/10.1186/1471-2164-11-655 | RIP/Repeat-Induced Point Mutation, Prediction, Fungi | Present (Jan 08 2025) | |
| Design-Island | https://doi.org/10.1186/1471-2164-9-150 | Genomic Island, Monte-Carlo, GC, Codon Usage | ||
| detectIR | https://doi.org/10.1371/journal.pone.0113349 | Inverted Repeat | Present (Jan 08 2025) | |
| detectMITE | https://doi.org/10.1038/srep19688 | Library Generation, MITE, ITR/TIR/DNA Transposon | Present (Jan 08 2025) | |
| detettore | https://doi.org/10.1111/nph.16308 | Polymorphism, Genotype, NGS/HTS, Paired-End | Present (Jan 08 2025) | |
| DeviaTE | https://doi.org/10.1111/1755-0998.13030 | NGS/HTS, Abundance, Visualization, Divergence | Present (Jan 08 2025) | |
| DGRscan | https://doi.org/10.3390/ijms150814234 | DGR/Diversity Generating Retroelement, Annotation | Present (Jan 08 2025) | |
| digIS | https://doi.org/10.1186/s12859-021-04177-6 | IS Element, HMM | Present (Jan 08 2025) | |
| DiGReF | https://doi.org/10.1186/1471-2164-13-430 | DGR/Diversity Generating Retroelement, Annotation | Absent (Jan 08 2025) | |
| dimorphicERV | https://doi.org/10.1186/s13100-018-0142-3 | NGS/HTS, Short-Read, Genotype, Polymorphism, ERV/Endogenous Retrovirus | Present (Jan 08 2025) | |
| discord-retro | https://arxiv.org/abs/1501.04268 | Illumina, Paired-End, NGS/HTS, Polymorphism, Genotype | Present (Jan 08 2025) | |
| DIVE | https://doi.org/10.1101/2022.06.13.495703 | De Novo, K-mer, Repeat | Present (Jan 08 2025) | |
| dnaasm | https://doi.org/10.7490/f1000research.1114626.1 | Repeat, NGS/HTS, De Novo | Present (Jan 08 2025) | |
| Dna-brnn | https://doi.org/10.1093/bioinformatics/btz264 | Satellite, Centromere, Neural Network | Present (Jan 08 2025) | |
| dnaPipeTE | https://doi.org/10.1093/gbe/evv050 | GitHub | NGS/HTS, Assembly, Annotation | Present (Jan 08 2025) |
| Domain Organizer | https://doi.org/10.1093/bioinformatics/btl337 | Alignment, HMM, Domain, Visualization | Absent (Jan 08 2025) | |
| Dotlet | https://doi.org/10.1093/bioinformatics/16.2.178 | Dot Plot, Visualization | Present (Jan 08 2025) | |
| dotmatcher | http://embossgui.sourceforge.net/demo/manual/dotmatcher.html | Dot Plot, Visualization | Present (Jan 08 2025) | |
| dotplot | Dot Plot, Visualization | Present (Jan 08 2025) | ||
| Dotter | https://doi.org/10.1016/0378-1119(95)00714-8 | Visualization, Dot Plot | Present (Jan 08 2025) | |
| DTExpress | https://doi.org/10.1007/978-1-0716-1134-0_2 | RNA-Seq, Expression | Present (Jan 08 2025) | |
| Duster | https://peercommunityjournal.org/articles/10.24072/pcjournal.68/ | Library Generation, Homology, K-mer | Present (Jan 08 2025) | |
| Dysgu | https://doi.org/10.1093/nar/gkac039 | NGS/HTS, Short-Read, Long-Read, Structural Variation | Present (Jan 08 2025) | |
| EAHelitron | https://doi.org/10.1186/s12859-019-2945-8 | Helitron, Structure | Present (Jan 08 2025) | |
| EarlGrey | https://doi.org/10.21203/rs.3.rs-1812599/v1 | Pipeline, Annotation, Repeat Masking, Homology, De Novo, Library Generation | Present (Jan 08 2025) | |
| Easymap | https://doi.org/10.3389/fpls.2021.655286 | Link | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (Jan 08 2025) |
| Ecc_finder | https://www.frontiersin.org/articles/10.3389/fpls.2021.743742/abstract | essDNA, NGS/HTS, Oxford Nanopore | Present (Jan 08 2025) | |
| ECCsplorer | https://doi.org/10.1186/s12859-021-04545-2 | eccDNA, Identification, Active TEs | Present (Jan 08 2025) | |
| EDTA | https://doi.org/10.1186/s13059-019-1905-y | Library Generation, Filtering, Structure, De Novo | Present (Jan 08 2025) | |
| EGID | https://doi.org/10.6026/007/97320630007311 | Genomic Island, Prediction | Absent (Jan 08 2025) | |
| ELAN | https://doi.org/10.1093/nar/gkr337 | Homology, Insertion Site, Consensus | Absent (Jan 08 2025) | |
| ELITE (Efficiently Locating Insertions of Transposable Elements) | https://doi.org/10.1145/3307339.3342182 | Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| EpiTEome | https://doi.org/10.1186/s13059-017-1232-0 | Polymorphism, Genotype, NGS/HTS, Methyl-Seq, Bisulfite, Methylation, | Present (Jan 08 2025) | |
| ERVcaller | https://doi.org/10.1093/bioinformatics/btz205 | ERV/Endogenous Retrovirus, Homo sapiens, NGS/HTS, Polymorphism, Genotype | Absent (Jan 08 2025) | |
| ERVmap | https://doi.org/10.1073/pnas.1814589115 | ERV/Endogenous Retrovirus, RNA-Seq, Transcriptome,Homo sapiens | Present (Jan 08 2025) | |
| ESAP Plus | https://doi.org/10.1186/s12864-016-3328-4 | Simple Sequence Repeat/Microsatellite, Expression, EST, Clustering, Repeat Masking | Absent (Jan 08 2025) | |
| ESMP | https://doi.org/10.6026/97320630008206 | Simple Sequence Repeat/Microsatellite, Expression, EST, Clustering | Absent (Jan 08 2025) | |
| ESSENTIALS | https://doi.org/10.1371/journal.pone.0043012 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Absent (Jan 08 2025) | |
| ExoPLOT | https://doi.org/10.1016/j.ygeno.2022.110434 | RNA-Seq, Expression, Transcription, NGS/HTS | Present (Jan 08 2025) | |
| ExpansionHunter | https://doi.org/10.1101/gr.225672.117 | Short Read, NGS/HTS, Short Tandem Repeat | Present (Jan 08 2025) | |
| ExpansionHunter Denovo | https://doi.org/10.1101/863035 | Short-Read, NGS/HTS, Short Tandem Repeat | Present (Jan 08 2025) | |
| ExplorATE | https://doi.org/10.1093/bioinformatics/btac354 | Expression, Transcription, RNA-Seq | Present (Jan 08 2025) | |
| FasTE | https://doi.org/10.1111/1755-0998.13489 | De Novo, Homology, Library Generation, Annotation, Pipeline, Classification | Present (Jan 08 2025) | |
| Fastq2LoxDel | https://doi.org/10.1101/2020.07.14.202044 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (Jan 08 2025) | |
| FASTQINS | https://doi.org/10.1093/nar/gkaa679 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism, Read Mapping | Present (Jan 08 2025) | |
| FindTelomeres | Telomere | Present (Jan 08 2025) | ||
| FiTnEss (Finding Tn-Seq Essentials) | https://doi.org/10.1073/pnas.1900570116 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (Jan 08 2025) | |
| FlexDotPlot | https://doi.org/10.1101/2020.04.03.023655 | Visualization, Dot Plot | Present (Jan 08 2025) | |
| FlexiDot | https://doi.org/10.1093/bioinformatics/bty395 | Visualization, Dot Plot | Present (Jan 08 2025) | |
| FORRepeats | https://doi.org/10.1093/bioinformatics/btf843 | Repeat, Detection | ||
| FullSSR | https://doi.org/10.1155/2016/6040124 | Simple Sequence Repeat/Microsatellite, Primer | Present (Jan 08 2025) | |
| GASVPro | https://doi.org/10.1186/gb-2012-13-3-r22 | Structural Variation, NGS/HTS,Paired-End | Absent (Jan 08 2025) | |
| GC-Profile | https://doi.org/10.2174/1389202915999140328163125 | Genomic Island, GC | Absent (Jan 08 2025) | |
| GeIST | https://doi.org/10.1093/bioinformatics/btv350 | Tn-Seq, Transposon Mutagenesis | Present (Jan 08 2025) | |
| Generic Repeat Finder | https://doi.org/10.1104/pp.19.00386 | LTR Retrotransposon, MITE, Inverted Repeat, ITR/TIR/DNA Transposon | Present (Jan 08 2025) | |
| GeneTEFlow | https://doi.org/10.1101/2020.04.28.065862 | RNA-Seq, NGS/HTS, Nextflow | Present (Jan 08 2025) | |
| geNomad | https://doi.org/10.1038/s41587-023-01953-y | Virus, Plasmid, Machine Learning, Detection, Classification | Present (Jan 08 2025) | |
| Genome ARTIST v2 | https://doi.org/10.3390/ijms232012686 | Tn-Seq, Transposon Mutagenesis, Drosophila, ITR/TIR/DNA Transposon | Present (Jan 08 2025) | |
| GenomeDiff | Dot Plot, Visualization, Virus | Present (Jan 08 2025) | ||
| GenomeTools | https://doi.ieeecomputersociety.org/10.1109/TCBB.2013.68 | Genome Annotation | Present (Jan 08 2025) | |
| Gepard | https://doi.org/10.1093/bioinformatics/btm039 | Visualization, Dot Plot | Present (Jan 08 2025) | |
| G-IMEx | https://doi.org/10.6026/97320630005221 | Simple Sequence Repeat/Microsatellite, Repeat Extraction, Annotation | Absent (Jan 08 2025) | |
| GI-Cluster | https://doi.org/10.1142/S0219720018400103 | Genomic Island, GC, Codon Usage, K-mer | Present (Jan 08 2025) | |
| GIDetector | https://doi.org/10.1186/1471-2164-11-S2-S1 | Genomic Island, Pipeline | Absent (Jan 08 2025) | |
| GIHunter | https://doi.org/10.4172/jpb.1000322 | Genomic Island, Prediction | Absent (Jan 08 2025) | |
| GI-POP | https://doi.org/10.1016/j.gene.2012.11.063 | Genomic Island, SVM, Annotation | Absent (Jan 08 2025) | |
| GIPSy | https://doi.org/10.1016/j.jbiotec.2015.09.008 | Genomic Island, GC, Homology, HMM | Present (Jan 08 2025) | |
| GIST | https://doi.org/10.6026/97320630008203 | Genomic Island, Pipeline | Absent (Jan 08 2025) | |
| GI-SVM | https://doi.org/10.1142/S0219720016400035 | Genomic Island, SVM, K-mer | Present (Jan 08 2025) | |
| GIV | https://doi.org/10.6026/97320630009879 | Genomic Island, Visualization | Absent (Jan 08 2025) | |
| GMATA | https://doi.org/10.3389/fpls.2016.01350 | Simple Sequence Repeat/Microsatellite, Repeat Extraction, Annotation, Primer | Present (Jan 08 2025) | |
| GMATo | https://doi.org/10.6026/97320630009541 | Simple Sequence Repeat/Microsatellite, Repeat Annotation | Present (Jan 08 2025) | |
| GPAC (Genome Presence/Absence Compiler) | https://doi.org/10.1093/molbev/msu276 | Polymorphism, Genotype | Present (Jan 08 2025) | |
| GraffiTE | https://doi.org/10.1101/2023.09.11.557209 | Polymorphism, Structural Variation, Long-Read, NGS/HTS, Assemblies, Pangenomes, Graph-Genome, Genotype | Present (Jan 08 2025) | |
| GraphTyper | https://doi.org/10.1038/ng.3964 | Structural Variation, Short-Read, NGS/HTS | Present (Jan 08 2025) | |
| GraphTyper2 | https://doi.org/10.1038/s41467-019-13341-9 | Structural Variation, Short-Read, NGS/HTS | Present (Jan 08 2025) | |
| GRASPER | https://doi.org/10.1089/cmb.2013.0129 | Structural Variation, Repeat, Homology, NGS/HTS, Paired-End | Present (Jan 08 2025) | |
| GREAM | https://doi.org/10.1371/journal.pone.0133647 | Mammal, Web Server,Genome, Analysis | Present (Jan 08 2025) | |
| Greedier | https://doi.org/10.1093/bioinformatics/btm613 | Homology, Repeat Masking,Nested Insertion, Graph | Present (Jan 08 2025) | |
| HashRepeatFinder | https://doi.org/10.1007/s12539-015-0119-6 | De Novo, Library Generation | Absent (Jan 08 2025) | |
| HDRSM (Highly Divergent Repeat Search Method) | https://doi.org/10.1186/s12859-021-03977-0 | SINE | Present (Jan 08 2025) | |
| HELIANO | https://doi.org/10.1101/2024.02.08.579435 | Helitron, Annotation | Present (Jan 08 2025) | |
| HelitronFinder | https://doi.org/10.1186/1471-2164-9-51 | Helitron, Structure | Absent (Jan 08 2025) | |
| HelitronScanner | https://doi.org/10.1073/pnas.1410068111 | Helitron, Structure | Present (Jan 08 2025) | |
| HelSearch | https://doi.org/10.1073/pnas.0905563106 | Helitron, Structure | Present (Jan 08 2025) | |
| HERA (Highly Efficient Repeat Assembly) | https://doi.org/10.1038/s41467-019-13355-3 | Long-Read, Graph, Assembly | ||
| HiC-TE | https://doi.org/10.1101/2021.12.18.473300 | Hi-C, NGS/HTS, Pipeline | Present (Jan 08 2025) | |
| HiTE | https://doi.org/10.1101/2023.05.23.541879 | Detection, Annotation | Present (Jan 08 2025) | |
| HiTea | https://doi.org/10.1101/2020.04.27.060145 | Hi-C, NGS/HTS, Genotype, Polymorphism | Present (Jan 08 2025) | |
| HIVIntact | https://doi.org/10.1186/s12977-021-00561-5 | Retrovirus, Activity | Present (Jan 08 2025) | |
| HMMER | https://doi.org/10.1371/journal.pcbi.1000069 | HMM | Present (Jan 08 2025) | |
| HomologMiner | https://doi.org/10.1093/bioinformatics/btm048 | Homology, Genome, Comparative | Absent (Jan 08 2025) | |
| HTdetect | https://doi.org/10.1093/gbe/evu026 | Horizontal Transfer, Homology | Present (Jan 08 2025) | |
| ICEfinder | https://doi.org/10.1093/nar/gky1123 | Link | ICE/Integrative and Conjugative Element, HMM | Present (Jan 08 2025) |
| ICEscreen | https://doi.org/10.1093/nargab/lqac079 | ICE/Integrative and Conjugative Element, HMM | Present (Jan 08 2025) | |
| IDSSR | https://doi.org/10.3390/ijms20143497 | Simple Sequence Repeat/Microsatellite, NGS/HTS, Paired-End, Primer, Repeat Annotation, Polymorphism | Present (Jan 08 2025) | |
| IGIPT | https://doi.org/10.6026/007/97320630007307 | Genomic Island, Nucleotide Composition, Visualization | Present (Jan 08 2025) | |
| iMapper | https://doi.org/10.1093/bioinformatics/btn541 | Genome, Ensembl, Transposon Mutagenesis | Present (Jan 08 2025) | |
| IMEx | https://doi.org/10.1093/bioinformatics/btm097 | Simple Sequence Repeat/Microsatellite, Annotation, Web Server | Absent (Jan 08 2025) | |
| iMGEins | https://doi.org/10.1186/s12864-018-5290-9 | NGS/HTS, Paired-End, Homology, Genotype, Polymorphism, Annotation | Present (Jan 08 2025) | |
| iMSAT | https://doi.org/10.1186/1471-2164-15-858 | Simple Sequence Repeat/Microsatellite, Illumina, NGS/HTS, Short-Read, Genotype, Polymorphism, Repeat Extraction | Present (Jan 08 2025) | |
| INDeGenIUS | https://doi.org/10.1007/s12038-010-0040-4 | Genomic Island, K-mer | ||
| inGAP-sv | https://doi.org/10.1093/nar/gkr506 | Structural Variation, NGS/HTS, Bayesian, Paired-End, Visualization | Present (Jan 08 2025) | |
| InFire | https://doi.org/10.1093/bioinformatics/btr672 | Transposon Mutagenesis, Web Server,Restriction Digestion | Absent (Jan 08 2025) | |
| InMut-Finder | https://doi.org/10.1186/s12864-021-08206-9 | NGS/HTS, Onxford Nanopore, Tn-Seq, Transposon Mutagenesis | Present (Jan 08 2025) | |
| Inpactor | https://doi.org/10.3390/biology7020032 | LTR Retrotransposon, Classification, Insertion Time | Present (Jan 08 2025) | |
| Inpactor2 | https://doi.org/10.1093/bib/bbac511 | LTR Retrotransposon, Classification, Insertion Time, Neural Network | Present (Jan 08 2025) | |
| InsertionMapper | https://doi.org/10.1186/1471-2164-14-679 | Tn-Seq, Transposon Mutagenesis, NGS/HTS | Present (Jan 08 2025) | |
| In-seq/Tn-seq | http://doi.org/10.1038/nprot.2011.417 | Tn-Seq, Transposon Mutagenesis | Present (Jan 08 2025) | |
| INSurVeyor | https://doi.org/10.1038/s41467-023-38870-2 | Polymorphism, Short-Reads, NGS/HTS, Paired-End | Present (Jan 08 2025) | |
| IntegronFinder | https://doi.org/10.1093/nar/gkw319 | Link | Integron, HMM | Present (Jan 08 2025) |
| IntegronFinder 2.0 | https://doi.org/10.3390/microorganisms10040700 | Integron, HMM | Present (Jan 08 2025) | |
| Invade | https://doi.org/10.1093/molbev/msz079 | Simulation, piRNA, Genome | Present (Jan 08 2025) | |
| IpiRId | https://doi.org/10.1371/journal.pone.0179787 | piRNA, SVM | Present (Jan 08 2025) | |
| IRescue | https://doi.org/10.1101/2022.09.16.508229 | Single-Cell, NGS/HTS, RNA-Seq, Expression, Transcription | Present (Jan 08 2025) | |
| IRF | https://doi.org/10.1101/gr.2542904 | Google drive link | Inverted Repeat, Library Generation | |
| IRplus | https://doi.org/10.1093/gbe/evad177 | Link | Inverted Repeat, Plastid, Webserver | Present (Jan 08 2025) |
| ISAbR_finder | IS Element, AMR/Antibiotic Resistance | Absent (Jan 08 2025) | ||
| ISCompare | https://doi.org/10.1093/g3journal/jkab181 | IS Element, Genotype, Polymorphism | Present (Jan 08 2025) | |
| IScan | https://doi.org/10.1093/nar/gkm597 | IS Element, Homology | Absent (Jan 08 2025) | |
| ISEScan | https://doi.org/10.1093/bioinformatics/btx433 | IS Element, HMM, Homology, Library Generation | Present (Jan 08 2025) | |
| IslandCafe | https://doi.org/10.1534/g3.119.400562 | Genomic Island | Present (Jan 08 2025) | |
| IslandPath-DIMOB | https://doi.org/10.1093/bioinformatics/bty095 | Genomic Island, HMM, Homology, K-mer | Present (Jan 08 2025) | |
| IslandPick | https://doi.org/10.1186/1471-2105-9-329 | Genomic Island, Homology, Comparative | Absent (Jan 08 2025) | |
| IslandViewer 4 | https://doi.org/10.1093/bioinformatics/btp030 | Genomic Island, Visualization, Web Server | Absent (Jan 08 2025) | |
| ISMapper | https://doi.org/10.1186/s12864-015-1860-2 | IS Element, Short-Read, NGS/HTS, Illumina, Paired-End, Polymorphism, Genotype | Present (Jan 08 2025) | |
| ISQuest | https://doi.org/10.1093/bioinformatics/btv388 | IS Element, NGS/HTS, Homology | Present (Jan 08 2025) | |
| ISsaga | https://doi.org/10.1186/gb-2011-12-3-r30 | Homology, Annotation, IS Element | Absent (Jan 08 2025) | |
| ISseeker | https://doi.org/10.1099/mgen.0.000062 | IS Element, Homology, Comparative | Present (Jan 08 2025) | |
| iSVP | https://doi.org/10.1186/1752-0509-7-s6-s8 | Structural Variation, Pipeline | Present (Jan 08 2025) | |
| ITIS (Identification of Transposon Insertion Sites) | https://doi.org/10.1186/s12859-015-0507-2 | Genotype, Polymorphism, NGS/HTS | Absent (Jan 08 2025) | |
| IUPACpal | https://doi.org/10.1186/s12859-021-03983-2 | Inverted Repeat | Present (Jan 08 2025) | |
| JDotter | https://doi.org/10.1093/bioinformatics/btg406 | Dot Plot, Visualization | Present (Jan 08 2025) | |
| Jitterbug | https://doi.org/10.1186/s12864-015-1975-5 | Paired-End, NGS/HTS, Polymorphism, Genotype, | Present (Jan 08 2025) | |
| KKSC Significance Test | https://doi.org/10.1371/journal.pcbi.1004812 | Polymorphism, Genotype, LINE/Non-LTR Retrotransposon, Age, Speciation | Present (Jan 08 2025) | |
| L1EM | https://doi.org/10.1093/bioinformatics/btz724 | Expression, Transcription, LINE1, LINE/Non-LTR Retrotransposon, Activity, NGS/HTS | Present (Jan 08 2025) | |
| L1PD (LINE-1 Pattern Detection) | https://doi.org/10.1186/s12859-022-04907-4 | LINE1, LINE/Non-LTR Retrotransposon, K-mer | Present (Jan 08 2025) | |
| L1Seq | https://doi.org/10.1101/gr.106419.110 | LINE/Non-LTR Retrotransposon, LINE1 | Present (Jan 08 2025) | |
| LAST | https://doi.org/10.1186/s13059-015-0670-9 | Alignment, Repeat | Absent (Jan 08 2025) | |
| LIONS | https://doi.org/10.1093/bioinformatics/btz130 | RNA-Seq, Transcription | Present (Jan 08 2025) | |
| LocaTR | https://doi.org/10.1186/s12864-016-3043-1 | LTR Retrotransposon, Homology, Structure, Annotation | Present (Jan 08 2025) | |
| LocusMasterTE | https://doi.org/10.1101/2023.03.21.533716 | NGS/HTS, Long-Read, Expression, Transcription, RNA-Seq | Present (Jan 08 2025) | |
| LongRepMarker | https://doi.org/10.1093/nar/gkab563 | De Novo, K-mer, Library Generation, Long-Read, Short-Read | Present (Jan 08 2025) | |
| Look4LTRs | https://doi.org/10.1186/s13100-024-00317-w | LTR Retrotransposon, Nested Insertion, Annotation | Present (Jan 08 2025) | |
| LoRTE | https://doi.org/10.1186/s13100-017-0088-x | Long-Read, PacBio, NGS/HTS, Genotype, Polymorphism, Indel,Homology | Absent (Jan 08 2025) | |
| LoRTIS-SS | https://doi.org/10.1101/2022.05.26.493556 | Long-Read, NGS/HTS, Oxford Nanopore, Tn-Seq, Transposon Mutagenesis | Present (Jan 08 2025) | |
| LTR_FINDER | https://doi.org/10.1093/nar/gkm286 | LTR Retrotransposon, Structure, Web Server | Absent (Jan 08 2025) | |
| LTR_FINDER_parallel | https://doi.org/10.1186/s13100-019-0193-0 | LTR Retrotransposon, Structure, HPC | Present (Jan 08 2025) | |
| LTR_MINER | https://doi.org/10.1186/gb-2004-5-10-r79 | LTR Retrotransposon, Solo-LTR, Filtering, Nested Insertion | ||
| LTR_par | https://www.ncbi.nlm.nih.gov/pubmed/16819780 | LTR Retrotransposon, Structure | ||
| LTR_retriever | https://doi.org/10.1104/pp.17.01310 | LTR Retrotransposon, Structure, Library Generation, Filtering | Present (Jan 08 2025) | |
| LTR_STRUC | https://doi.org/10.1093/bioinformatics/btf878 | LTR Retrotransposon, Structure | Present (Jan 08 2025) | |
| LTR Annotator | https://doi.org/10.17706/ijbbb.2015.5.3.165-174 | LTR Retrotransposon, Library Generation, Annotation | ||
| LTRclassifier | https://doi.org/10.1080/2159256X.2016.1241050 | Link | LTR Retrotransposon, HMM, Classification, Web Server | Present (Jan 08 2025) |
| LtrDetector | https://doi.org/10.1186/s12864-019-5796-9 | De Novo, LTR Retrotransposon, Structure, Annotation, Visualization | Present (Jan 08 2025) | |
| LTRdigest | https://doi.org/10.1093/nar/gkp759 | LTR Retrotransposon, Web Server, Structure, Classification | Present (Jan 08 2025) | |
| LTRharvest | https://doi.org/10.1186/1471-2105-9-18 | Link | LTR Retrotransposon, Structure | Present (Jan 08 2025) |
| LTRphyler | https://doi.org/10.1186/1471-2229-13-172 | LTR Retrotransposon, Classification | Absent (Jan 08 2025) | |
| ltr.pl | https://doi.org/10.1186/1471-2164-8-90 | De Novo, LTR Retrotransposon, HMM | Absent (Jan 08 2025) | |
| LTRpred | https://doi.org/10.21105/joss.02170 | De Novo, Homology, LTR Retrotransposon, Annotation | Present (Jan 08 2025) | |
| LTRsift | https://doi.org/10.1186/1759-8753-3-18 | Link | De Novo, LTR Retrotransposon, Visualization, Library Generation, Annotation | Absent (Jan 08 2025) |
| LTRtype | https://doi.org/10.3389/fpls.2017.00402 | LTR Retrotransposon, Nested Insertion, Homology, | Absent (Jan 08 2025) | |
| Lumpy | https://doi.org/10.1186/gb-2014-15-6-r84 | Structural Variation | Present (Jan 08 2025) | |
| MacSyFinder | https://doi.org/10.1371/journal.pone.0110726 | CRISPR, HMM | Present (Jan 08 2025) | |
| MAGenTA | https://doi.org/10.1093/bioinformatics/btx320 | Web Server, Tn-Seq, Transposon Mutagenesis, NGS/HTS, Visualization, Analysis | Present (Jan 08 2025) | |
| MANTIS | http://doi.org/10.18632/oncotarget.13918 | Simple Sequence Repeat/Microsatellite, Instability, Cancer, NGS/HTS | Present (Jan 08 2025) | |
| MASiVE | https://doi.org/10.1093/bioinformatics/btq454 | LTR Retrotransposon, Sirevirus, Structure, Repeat Extraction | Absent (Jan 08 2025) | |
| McClintock | https://doi.org/10.1534/g3.117.043893 | Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| McClintock2 | https://doi.org/10.1101/2023.02.13.528343 | Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| MCHelper | https://doi.org/10.1101/2023.10.17.562682 | Automated Curation, Classification | Present (Jan 08 2025) | |
| MEGAnE | https://doi.org/10.1101/2022.03.25.485726 | Github | Genotype, Polymorphism, NGS/HTS, Short-Read | Present (Jan 08 2025) |
| MegaLTR | https://doi.org/10.3389/fpls.2023.1237426 | Webserver | LTR Retrotransposon, Detection, Annotation, Webserver, Pipeline | Present (Jan 08 2025) |
| MELT | https://doi.org/10.1101/gr.218032.116 | Genotype, Polymorphism, Illumina, Paired-End, NGS/HTS | Present (Jan 08 2025) | |
| ME-Scan | https://doi.org/10.1186/s13100-020-00207-x | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (Jan 08 2025) | |
| MetaCompare | https://doi.org/10.1093/femsec/fiy079 | NGS/HTS, Metagenomics, AMR/Antibiotic Resistance, BLAST, Pathogen | Present (Jan 08 2025) | |
| MetaPhage | https://doi.org/10.1101/2022.04.17.488583 | NGS/HTS, Metagenomics, Annotation, Classification, Prophage/Bacteriophage | Present (Jan 08 2025) | |
| mer-engine | https://doi.org/10.1101/gr.1350803 | Repeat, De Novo, Library Generation | ||
| mge-cluster | https://doi.org/10.1093/nargab/lqad066 | Gitlab | Plasmid, Classification | Absent (Jan 08 2025) |
| MGERT | https://doi.org/10.1186/s13100-019-0163-6 | Conserved Domain, Repeat Extraction, De Novo, Library Generation, Repeat Extraction | Present (Jan 08 2025) | |
| MGEfinder | https://doi.org/10.1016/j.chom.2019.10.022 | Archaea, Bacteria,, NGS/HTS, Polymorphism, Library Generation | Present (Jan 08 2025) | |
| MGEScan | https://doi.org/10.1093/bioinformatics/btw157 | Web Server, LTR Retrotransposon, LINE/Non-LTR Retrotransposon, HMM | Present (Jan 08 2025) | |
| micRocounter | https://doi.org/10.1534/g3.119.400335 | Simple Sequence Repeat/Microsatellite, Annotation | Present (Jan 08 2025) | |
| MiMSI | https://doi.org/10.1101/2020.09.16.299925 | Simple Sequence Repeat/Microsatellite, Cancer | Present (Jan 08 2025) | |
| MindTheGap | https://doi.org/10.1093/bioinformatics/btu545 | NGS/HTS, Polymorphism, Genotype, K-mer | Present (Jan 08 2025) | |
| MIRU-profiler | https://doi.org/10.7717/peerj.5090 | Tuberculosis, Genotype, Tandem Repeat | Present (Jan 08 2025) | |
| MIRU-VNTRplus | https://doi.org/10.1093/nar/gkq351 | Tuberculosis, Genotype, Tandem Repeat, Web Server | Present (Jan 08 2025) | |
| MISA | https://doi.org/10.1007/s00122-002-1031-0 | Simple Sequence Repeat/Microsatellite, Annotation | ||
| MISA-web | https://doi.org/10.1093/bioinformatics/btx198 | Simple Sequence Repeat/Microsatellite, Annotation | Present (Jan 08 2025) | |
| MAK (MITE Analysis Kit) | https://doi.org/10.1093/nar/gkg531 | MITE, Homology, Annotation, ITR/TIR/DNA Transposon | Absent (Jan 08 2025) | |
| MITE Digger | https://doi.org/10.1186/1471-2105-14-186 | MITE, Homology, Annotation, ITR/TIR/DNA Transposon | Absent (Jan 08 2025) | |
| MITE Tracker | https://doi.org/10.1186/s12859-018-2376-y | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Present (Jan 08 2025) | |
| MiteFinder | https://doi.org/10.1109/BIBM.2017.8217644 | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Present (Jan 08 2025) | |
| MiteFinderII | https://doi.org/10.1186/s12920-018-0418-y | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Present (Jan 08 2025) | |
| MITE-Hunter | https://doi.org/10.1093/nar/gkq862 | MITE, Structure, Annotation, ITR/TIR/DNA Transposon | Present (Jan 08 2025) | |
| MJSD | https://doi.org/10.1093/nar/gkp576 | Genomic Island, Nucleotide Composition | ||
| MobileElementFinder | https://doi.org/10.1093/jac/dkaa390 | IS Element, AMR/Antibiotic Resistance, Plasmid, Homology, Web Server | Absent (Jan 08 2025) | |
| MobilomeFINDER | https://doi.org/10.1093/nar/gkm380 | Genomic Island, Microarray, Web Server | Absent (Jan 08 2025) | |
| MOBSTER | https://doi.org/10.1186/s13059-014-0488-x | NGS/HTS, Genotype, Polymorphism, | Present (Jan 08 2025) | |
| ModuleOrganizer | https://doi.org/10.1186/1471-2105-11-474 | Sequence Motif, Visualization, Web Server | ||
| mosaicFlye | https://doi.org/10.1101/2020.01.15.908285 | NGS/HTS, Long-Read, Mosaic Repeat, Segmental Duplication, Assembly | Present (Jan 08 2025) | |
| mreps | https://doi.org/10.1093/nar/gkg617 | Tandem Repeat, De Novo, Library Generation | Present (Jan 08 2025) | |
| MSGIP | https://doi.org/10.1371/journal.pone.0146352 | Genomic Island, Mean Shift Algorithm | Present (Jan 08 2025) | |
| MTGIpick | https://doi.org/10.1093/bib/bbw118 | Genomic Island, K-mer | Present (Jan 08 2025) | |
| msatcommander | https://doi.org/10.1111/j.1471-8286.2007.01884.x | Simple Sequence Repeat/Microsatellite, Primer | Present (Jan 08 2025) | |
| msatfinder | Link | Simple Sequence Repeat/Microsatellite, Primer, Annotation, Repeat Extraction | Present (Jan 08 2025) | |
| mSINGS | https://doi.org/10.1373/clinchem.2014.223677 | Simple Sequence Repeat/Microsatellite, Instability, Polymorphism, Genotype, NGS/HTS, Cancer | Present (Jan 08 2025) | |
| MSIsensor | https://doi.org/10.1093/bioinformatics/btt755 | Simple Sequence Repeat/Microsatellite, Instability, Polymorphism, Genotype, NGS/HTS, Cancer | Present (Jan 08 2025) | |
| MUST | https://doi.org/10.1016/j.gene.2009.01.019 | MITE, Structure, Annotation, ITR/TIR/DNA Transposon | ||
| MUSTv2 | https://doi.org/10.1515/jib-2017-0029 | MITE, Structure, Annotation, ITR/TIR/DNA Transposon | Present (Jan 08 2025) | |
| MyDGR | https://doi.org/10.1093/nar/gkz329 | DGR/Diversity Generating Retroelement, Annotation, BLAST, Alignment, Web Server | Present (Jan 08 2025) | |
| NanoCasTE | https://doi.org/10.1111/jipb.13555 | NGS/HTS, Oxford Nanopore, Cas9, Polymorphism, Genotype | Present (Jan 08 2025) | |
| nanomonsv | https://doi.org/10.1101/2020.07.22.214262 | Structural Variation, NGS/HTS, Long-Read, Cancer | Present (Jan 08 2025) | |
| NanoSatellite | https://doi.org/10.1186/s13059-019-1856-3 | NGS/HTS, Oxford Nanopore, Tandem Repeat | Present (Jan 08 2025) | |
| nanotei | https://doi.org/10.3390/plants10122681 | NGS/HTS, Oxford Nanopore, Polymorphism, Genotype | Present (Jan 08 2025) | |
| NanoTRF | https://doi.org/10.3390/plants11162103 | NGS/HTS, Oxford Nanopore, Tandem Repeat | Present (Jan 08 2025) | |
| NanoVar | https://doi.org/10.1186/s13059-020-01968-7 | NGS/HTS, Oxford Nanopore, Polymorphism, Genotype | Present (Jan 08 2025) | |
| NanoWgsTE | https://doi.org/10.1101/2021.06.11.448052 | Oxford Nanopore, CRISPR, Eukaryotic Transposon | Present (Jan 08 2025) | |
| NCRF | https://doi.org/10.1093/bioinformatics/btz484 | Long-Read, NGS/HTS, Tandem Repeat, De Novo | Present (Jan 08 2025) | |
| ncRNAclassifier | https://doi.org/10.1186/1471-2105-13-246 | ncRNA, miRNA | Present (Jan 08 2025) | |
| NearTrans | https://doi.org/10.1007/978-3-319-78723-7_32 | Expression, Transcription, Analysis, Pipeline | ||
| nf-repeatmasking | http://doi.org/10.5281/zenodo.1134750 | Repeat Masking, Classification | Present (Jan 08 2025) | |
| NGSEP (Next-Generation Sequencing Experience Platform) | https://doi.org/10.1002/aps3.11520 | Github | NGS/HTS, Homology, Long-Read, Annotation | Present (Jan 08 2025) |
| ngs_te_mapper | https://doi.org/10.1371/journal.pone.0030008 | Target Site Duplication, Homology, NGS/HTS | Present (Jan 08 2025) | |
| NGSEP | https://doi.org/10.1002/aps3.11520 | https://sourceforge.net/projects/ngsep/ | Repeat Masking, Annotation | Present (Jan 08 2025) |
| ntHits | https://doi.org/10.1371/journal.pone.0030008 | K-mer, Repeat | Present (Jan 08 2025) | |
| NTRFinder | https://doi.org/10.1093/nar/gkr1070 | Tandem Repeat | ||
| OASIS | https://doi.org/10.1101/2020.11.02.365809 | IS Element, Homology, Classification | Present (Jan 08 2025) | |
| OMWSA (Optimized Moving Window Spectral Analysis) | https://doi.org/10.1093/bioinformatics/btm008 | Visualization, Repeat | Present (Jan 08 2025) | |
| One_code_to_find_them_all | https://doi.org/10.1186/1759-8753-5-13 | Repeat Extraction, Abundance | Present (Jan 08 2025) | |
| oriTfinder | https://doi.org/10.1093/nar/gky352 | Origin of Transfer, Plasmid, ICE/Integrative and Conjugative Element | Present (Jan 08 2025) | |
| OSTRFPD | https://doi.org/10.1177%2F1176934319843130 | Simple Sequence Repeat/Microsatellite, Alignment, Repeat Extraction, Annotation | Present (Jan 08 2025) | |
| packFinder | https://doi.org/10.1101/2021.06.18.448592 | Link | ITR/TIR/DNA Transposon, MuDR/Mutator, Pack-MULE | Present (Jan 08 2025) |
| PacmonSTR | https://doi.org/10.1093/bioinformatics/btu437 | Tandem Repeat, NGS/HTS, Long-Read, HMM,Homology | Present (Jan 08 2025) | |
| PADLOC (Prokaryotic Antiviral Defence LOCator) | https://doi.org/10.1093/nar/gkac400 | Webserver, Antiviral, Virus | Present (Jan 08 2025) | |
| PAI-IDA | https://doi.org/10.1016/S0378-1097(03)00204-0 | Genomic Island, GC, Codon Usage | ||
| PaliDIS | https://doi.org/10.1099/mgen.0.000917 | IS Element, Metagenomics, Annotation | Present (Jan 08 2025) | |
| panGRP | https://doi.org/10.1093/bioinformatics/btaa792 | Genomic Island | Present (Jan 08 2025) | |
| panISa | https://doi.org/10.1093/bioinformatics/bty479 | De Novo, IS Element, NGS/HTS, Short-Read, Annotation, Homology | Present (Jan 08 2025) | |
| Paragraph | https://doi.org/10.1186/s13059-019-1909-7 | Graph, Structural Variation, Genotype, NGS/HTS, Short-Read | Present (Jan 08 2025) | |
| ParasiTE | https://doi.org/10.1101/2022.09.21.507229 | Long-Read, NGS/HTS, RNA-Seq, Expression, Transcription | Present (Jan 08 2025) | |
| PASTEC | https://doi.org/10.1371/journal.pone.0091929 | Link | Classification | Present (Jan 08 2025) |
| PAtChER | https://doi.org/10.1101/2021.08.25.457666 | ChIP-Seq | Present (Jan 08 2025) | |
| PATIMDB | https://doi.org/10.1002/0471142727.mb1907s86 | Tn-Seq, Transposon Mutagenesis | Absent (Jan 08 2025) | |
| P-Clouds | https://doi.org/10.1016/j.ab.2008.05.015 | De Novo, Library Generation | ||
| PerSVade | https://doi.org/10.1101/2021.11.23.469703 | Structural Variation, Pipeline | Present (Jan 08 2025) | |
| PeSV-Fisher | https://doi.org/10.1371/journal.pone.0063377 | Structural Variation | ||
| PHACTS | https://doi.org/10.1093/bioinformatics/bts014 | Prophage/Bacteriophage, Classification | Present (Jan 08 2025) | |
| PhageAI | https://doi.org/10.1101/2020.07.11.198606 | Prophage/Bacteriophage, Web Server, Machine Learning, Classification | Present (Jan 08 2025) | |
| Phage Commander | https://doi.org/10.1101/2020.11.11.378802 | Prophage/Bacteriophage, Pipeline | Present (Jan 08 2025) | |
| Phage_Finder | https://doi.org/10.1093/nar/gkl732 | Prophage/Bacteriophage, Homology, HMM | Present (Jan 08 2025) | |
| PhaGenus | https://doi.org/10.1093/bib/bbad408 | Prophage/Bacteriophage, Classification | Present (Jan 08 2025) | |
| PhageWeb | https://doi.org/10.3389/fgene.2018.00644 | Prophage/Bacteriophage, Web Server, GC, tRNA | Absent (Jan 08 2025) | |
| PHAST | https://doi.org/10.1093/nar/gkr485 | Prophage/Bacteriophage, Web Server, Homology, Annotation, Visualization | Absent (Jan 08 2025) | |
| PHASTER | https://doi.org/10.1093/nar/gkw387 | Prophage/Bacteriophage, Web Server, Homology, Annotation, Visualization | Present (Jan 08 2025) | |
| Phigaro | https://doi.org/10.1093/bioinformatics/btaa250 | Prophage/Bacteriophage, Annotation | Present (Jan 08 2025) | |
| PhiSpy | https://doi.org/10.1093/nar/gks406 | Prophage/Bacteriophage, Homology | Present (Jan 08 2025) | |
| Phobos | Simple Sequence Repeat/Microsatellite, Library Generation | Present (Jan 08 2025) | ||
| phRAIDER | https://doi.org/10.1093/bioinformatics/btw258 | De Novo,Library Generation | Present (Jan 08 2025) | |
| PhyLTR | LTR Retrotransposon, Annotation, Pipeline, Gene Conversion, Classification, Phylogeny | Present (Jan 08 2025) | ||
| Piano | https://doi.org/10.1186/s12859-014-0419-6 | piRNA, SVM, Classification, Web Server | Absent (Jan 08 2025) | |
| PIATEA | HMM, Annotation Track | Present (Jan 08 2025) | ||
| Pibomd | https://doi.org/10.1039/c4mb00447g | piRNA, SVM | ||
| PILER | https://doi.org/10.1093/bioinformatics/bti1003 | De Novo, Library Generation | Present (Jan 08 2025) | |
| PILFER | https://doi.org/10.1016/j.ygeno.2017.12.005 | piRNA, RNA-Seq, NGS/HTS | Present (Jan 08 2025) | |
| PIMMS (Pragmatic Insertional Mutation Mapping System) | https://doi.org/10.3389/fgene.2015.00139 | NGS/HTS, Tn-Seq | Present (Jan 08 2025) | |
| Pindel | https://doi.org/10.1093/bioinformatics/btp394 | Short-Read, Paired-End, Structural Variation, NGS/HTS | Present (Jan 08 2025) | |
| PingPongPro | https://doi.org/10.1093/bioinformatics/bty578 | piRNA, RNA-Seq, NGS/HTS | Present (Jan 08 2025) | |
| piPipes | https://doi.org/10.1093/bioinformatics/btu647 | piRNA, RNA-Seq, ChIP-Seq, NGS/HTS | Present (Jan 08 2025) | |
| PIPS | https://doi.org/10.1371/journal.pone.0030848 | Genomic Island, Pathogenicity Island, Prediction | Absent (Jan 08 2025) | |
| PiRATE | https://doi.org/10.1186/s12864-018-4763-1 | Web Server, Homology, HMM, Structure, De Novo, Classification, Library Generation, Annotation | Present (Jan 08 2025) | |
| piRNA Pipeline | https://doi.org/10.1093/nar/gky761 | piRNA, NGS/HTS | Present (Jan 08 2025) | |
| piRNN | https://doi.org/10.7717/peerj.5429 | piRNA, K-mer, Convolutional Neural Network | Present (Jan 08 2025) | |
| piRPred | https://doi.org/10.1093/bioinformatics/btu441 | piRNA, SVM | Present (Jan 08 2025) | |
| piRNAPredictor | https://doi.org/10.1186/s12859-016-1206-3 | piRNA, Prediction | Present (Jan 08 2025) | |
| Plasflow | https://doi.org/10.1093/nar/gkx1321 | Plasmid, Metagenomics, Neural Network | Present (Jan 08 2025) | |
| PlasmidFinder | https://doi.org/10.1128/aac.02412-14 | Plasmid, Homology | Absent (Jan 08 2025) | |
| PlasForest | https://doi.org/10.1186/s12859-021-04270-w | Plasmid, Homology, Classification | Present (Jan 08 2025) | |
| PlasmidHunter | https://doi.org/10.1101/2023.02.01.526640 | Link | Plasmid, Webserver | Present (Jan 08 2025) |
| PlasmidTron | https://doi.org/10.1099/mgen.0.000164 | Plasmid, K-mer | Present (Jan 08 2025) | |
| PlasLR | https://doi.org/10.1101/2021.06.14.448306 | Plasmid, Long-Read | Present (Jan 08 2025) | |
| PlasTrans | https://doi.org/10.1099/mgen.0.000459 | Plasmid | Present (Jan 08 2025) | |
| PlotRep | https://doi.org/10.1093/nar/gkl263 | Dot Plot, Visualization, Repeat Merging | Absent (Jan 08 2025) | |
| polyCRACKER | https://doi.org/10.1186/s12864-019-5828-5 | Polyploid, Subgenome | ||
| polyDetect | https://doi.org/10.1186/s13100-018-0118-3 | NGS/HTS, Polymorphism, Short-Read, Alu, SINE, Homo sapiens, Genotype, Population Genomics | Present (Jan 08 2025) | |
| polymorphicHERV | https://doi.org/10.1371/journal.pcbi.1006564 | ERV/Endogenous Retrovirus, K-mer, Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| PolyMorphPredict | https://doi.org/10.3389/fpls.2018.01966 | Simple Sequence Repeat/Microsatellite, Primer, Web Server | Present (Jan 08 2025) | |
| PoPoolationTE | https://doi.org/10.1093/molbev/msw137 | Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| PostSV | https://doi.org/10.1177/1177932219892957 | Structural Variation, NGS/HTS, SVM | ||
| PPR-Meta | https://doi.org/10.1093/gigascience/giz066 | Link | Prophage/Bacteriophage, Plasmid, Deep Learning | Absent (Jan 08 2025) |
| PRAP | https://doi.org/10.1093/bioinformatics/btt482 | De Novo, Library Generation, Repeat Masking, Archaea, Bacteria | Present (Jan 08 2025) | |
| PredictBias | https://content.iospress.com/articles/in-silico-biology/isb00352 | Genomic Island, Web Server, Homology | Present (Jan 08 2025) | |
| Process_hits | https://doi.org/10.1186/1756-0500-4-482 | Repeat Extraction, Alignment | Present (Jan 08 2025) | |
| ProGeRF | http://doi.org/10.1155/2015/394157 | Simple Sequence Repeat/Microsatellite, Annotation | Absent (Jan 08 2025) | |
| Prophage Finder | https://content.iospress.com/articles/in-silico-biology/isb00235 | Prophage/Bacteriophage, Homology | ||
| ProphET | https://doi.org/10.1371/journal.pone.0223364 | Prophage/Bacteriophage, Homology, Annotation | Present (Jan 08 2025) | |
| Prophinder | https://doi.org/10.1093/bioinformatics/btn043 | Prophage/Bacteriophage, Homology | Absent (Jan 08 2025) | |
| proTRAC | https://doi.org/10.1186/1471-2105-13-5 | piRNA | Absent (Jan 08 2025) | |
| PSSV | https://doi.org/10.1093/bioinformatics/btw605 | Structural Variation, NGS/HTS | Absent (Jan 08 2025) | |
| PTEMD | https://doi.org/10.1093/dnares/dsw011 | Short-Read, NGS/HTS, Genotype, Polymorphism, De Novo | Absent (Jan 08 2025) | |
| Pysim-sv | https://doi.org/10.1186/s12859-017-1464-8 | Structural Variation, NGS/HTS, Simulation | Present (Jan 08 2025) | |
| QDD | https://doi.org/10.1093/bioinformatics/btp670 | Simple Sequence Repeat/Microsatellite, Primer | Absent (Jan 08 2025) | |
| RAIDER | https://doi.org/10.1007/978-3-319-02624-4_16 | De Novo, Repeat, Library Generation | ||
| rampage_alu | https://doi.org/10.1101/gr.249789.119 | RNA-Seq, Expression, Alu, SINE, RAMPAGE, NGS/HTS, Paired-End | Present (Jan 08 2025) | |
| RAP | https://doi.org/10.1093/bioinformatics/bti039 | De Novo, Annotation | ||
| RAPTR-SV | https://doi.org/10.1093/bioinformatics/btv086 | Structural Variation, NGS/HTS, Illumina, Paired-End | Present (Jan 08 2025) | |
| RAREFAN (RAyt/REpin Finder and ANalyzer) | https://doi.org/10.24072/pcjournal.244 | Webserver, REPIN/RAYT, Annotation | Present (Jan 08 2025) | |
| RBR | https://doi.org/10.1093/bioinformatics/btl368 | Expression, Transcription, RNA-Seq, Repeat Masking, De Novo | Present (Jan 08 2025) | |
| rCANID | https://doi.org/10.1109/TNB.2019.2908438 | Long-Read, NGS/HTS, Genotype, Polymorphism, Structural Variation | Present (Jan 08 2025) | |
| read2marker | https://doi.org/10.2144/000112025 | Simple Sequence Repeat/Microsatellite, Primer | ||
| REannotate | https://doi.org/10.1186/1471-2164-9-614 | Annotation Parsing, Nested Insertion | Present (Jan 08 2025) | |
| ReAlignerV | https://doi.org/10.1186/1471-2105-9-112 | Alignment | ||
| ReAS | https://doi.org/10.1371/journal.pcbi.0010043 | Email for files: ReAS@genomics.org.cn | De Novo, Library Generation, NGS/HTS | |
| Red | https://doi.org/10.1186/s12859-015-0654-5 | Machine Learning, De Novo, Library Generation | ||
| REdiscoverTE | https://doi.org/10.1038/s41467-019-13035-2 | Expression, Transcription, RNA-Seq | Present (Jan 08 2025) | |
| ReDoSt | https://doi.org/10.1186/1471-2164-12-621 | DIRS, Eukaryotic Retrotransposon, Homology, Structure, Annotation | Absent (Jan 08 2025) | |
| RelocaTE2 | https://doi.org/10.7717/peerj.2942 | Polymorphism, Genotype, NGS/HTS | Present (Jan 08 2025) | |
| RepAHR | https://doi.org/10.1186/s12859-020-03779-w | De Novo, Library Generation, NGS/HTS, K-mer | Present (Jan 08 2025) | |
| RepARK | https://doi.org/10.1093/nar/gku210 | De Novo, Library Generation, NGS/HTS | Present (Jan 08 2025) | |
| RepBox | https://doi.org/10.1186/s12859-023-05419-5 | TE detection, TE annotation, Plants | Present (Jan 08 2025) | |
| REPCLASS | https://uta-ir.tdl.org/uta-ir/handle/10106/455 | Classification | Present (Jan 08 2025) | |
| REPdenovo | https://doi.org/10.1371/journal.pone.0150719 | Short-Read, NGS/HTS, De Novo, Assembly | Present (Jan 08 2025) | |
| RepeatAnalyzer | https://doi.org/10.1186/s12864-016-2686-2 | Simple Sequence Repeat/Microsatellite, Summary, Genotype | Present (Jan 08 2025) | |
| RepeatCraft | https://doi.org/10.1093/bioinformatics/bty745 | Nested Insertion, Visualization | Present (Jan 08 2025) | |
| Repeat Enrichment Estimator | https://doi.org/10.1186/gb-2010-11-6-r69 | NGS/HTS, ChIP-Seq, Repeat, Webserver | Absent (Jan 08 2025) | |
| Repeat Expansion Viewer (REViewer) | Short Read, NGS/HTS, Short Tandem Repeat | Present (Jan 08 2025) | ||
| RepeatExplorer | https://doi.org/10.1093/bioinformatics/btt054 | Link | De Novo, Library Generation, Annotation, NGS/HTS | Present (Jan 08 2025) |
| RepeatFiller | https://doi.org/10.1093/gigascience/giz132 | Genome Alignment, Repeat | Present (Jan 08 2025) | |
| RepeatFinder | https://doi.org/10.1186/gb-2001-2-8-research0027 | Library Generation | Present (Jan 08 2025) | |
| RepeatGluer | https://doi.org/10.1101/gr.2395204 | Repeat Annotation | ||
| RepeatMasker | Repeat Masking, Annotation | Present (Jan 08 2025) | ||
| RepeatModeler | https://doi.org/10.1073/pnas.1921046117 | GitHub | De Novo, Library Generation, Structure, Seed Alignment, Classification | Absent (Jan 08 2025) |
| RepeatProfiler | https://doi.org/10.1101/2020.05.22.111252 | NGS/HTS, Short-Read, Visualization, Repeat | Present (Jan 08 2025) | |
| repeatR | Eukaryotic Transposon, RepeatMasker, Annotation, Summary | Present (Jan 08 2025) | ||
| RepeatRunner | https://doi.org/10.1016/j.gene.2006.09.011 | De Novo, Library Generation | Present (Jan 08 2025) | |
| RepeatScout | https://doi.org/10.1093/bioinformatics/bti1018 | De Novo, Library Generation | Present (Jan 08 2025) | |
| RepeatSeq | https://doi.org/10.1093/nar/gks981 | Simple Sequence Repeat/Microsatellite, Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| RepBox | https://doi.org/10.1186/s12859-023-05419-5 | Detection, Annotation, Classification, Pipeline | Present (Jan 08 2025) | |
| RepEnrich | https://doi.org/10.1186/1471-2164-15-583 | NGS/HTS, RNA-Seq, Expression | Present (Jan 08 2025) | |
| RepEnrich2 | NGS/HTS, RNA-Seq, Expression | Present (Jan 08 2025) | ||
| REPET | https://doi.org/10.1371/journal.pone.0016526 | Link | De Novo, Homology, Structure, Library Generation, Annotation | Present (Jan 08 2025) |
| RepExpress | https://doi.org/10.1002/cpz1.206 | Pipeline, RNA-Seq, Expression | Present (Jan 08 2025) | |
| Repguide | CRISPR, gRNA, Repeat | Present (Jan 08 2025) | ||
| RepLoc | https://doi.org/10.1093/bib/bbaa086 | Repeat, K-mer, Visualization, Annotation, Web Server | Present (Jan 08 2025) | |
| RepLong | https://doi.org/10.1093/bioinformatics/btx717 | De Novo, Long-Read, NGS/HTS | Present (Jan 08 2025) | |
| RepMiner | https://doi.org/10.1101/gr.083360.108 | Repeat, Library Generation, De Novo | Present (Jan 08 2025) | |
| Repseek | https://doi.org/10.1093/bioinformatics/btl519 | Repeat, Library Generation, De Novo | Absent (Jan 08 2025) | |
| RepSeeker | https://ieeexplore.ieee.org/document/5260704 | Repeat, Library Generation, De Novo | ||
| REPuter | https://doi.org/10.1093/nar/29.22.4633 | Repeat, Library Generation, De Novo | Present (Jan 08 2025) | |
| reputils | Github | TE Identification, Alignment, MSA, Manual Curation | Present (Jan 08 2025) | |
| Repsc | Expression, RNA-Seq, Single Cell | Present (Jan 08 2025) | ||
| RetroMap | https://doi.org/10.1186/gb-2004-5-10-r78 | LTR Retrotransposon, Visualization | Present (Jan 08 2025) | |
| retroSeeker | https://doi.org/10.1007/s44307-023-00005-5 | Eukaryotic Retrotransposon, Detection, Homology | Present (Jan 08 2025) | |
| Retroseq | https://doi.org/10.1093/bioinformatics/bts697 | Genotype, Polymorphism, NGS/HTS, Illumina, Paired-End | Present (Jan 08 2025) | |
| RetroSnake | https://doi.org/10.1101/2022.04.08.487607 | NGS/HTS, Endogenous Retrovirus, Annotation | Present (Jan 08 2025) | |
| RetroSom | https://doi.org/10.1101/660779 | Machine Learning, NGS/HTS, Genotype, Polymorphism | Present (Jan 08 2025) | |
| RetroTector | https://doi.org/10.1093/nar/gkm515 | ERV/Endogenous Retrovirus | Present (Jan 08 2025) | |
| retrotransposons-spread | https://doi.org/10.1093/bioinformatics/btw622 | Simulation, LTR Retrotransposon | Present (Jan 08 2025) | |
| REViewer | https://doi.org/10.1016/j.ygeno.2013.07.008 | Email for link: reviewer_info@kaist.ac.kr | Visualization, Annotation, Homology | |
| REViewer (Repeat Expansion Viewer) | https://doi.org/10.1186/s13073-022-01085-z | Link | Tandem Repeat, NGS/HTS, Visualization | Present (Jan 08 2025) |
| RFPlasmid | https://doi.org/10.1101/2020.07.31.230631 | Link | Plasmid, Resistance, AMR/Antibiotic Resistance, K-mer, Homology | Present (Jan 08 2025) |
| RIPCAL | https://doi.org/10.1186/1471-2105-9-478 | RIP/Repeat-Induced Point Mutation, Mutation, Alignment, Repeat | Present (Jan 08 2025) | |
| RISCI (Repeat Induced Sequence Changes Identifier) | https://doi.org/10.1186/1471-2105-11-609 | NGS/HTS, Genotype, Polymorphism | Present (Jan 08 2025) | |
| RJPrimers | https://doi.org/10.1093/nar/gkq425 | Homology, Primer | Absent (Jan 08 2025) | |
| rMFilter | https://doi.org/10.1093/bioinformatics/btx279 | NGS/HTS, Structural Variation, Long-Read | Present (Jan 08 2025) | |
| rMETL | https://doi.org/10.1093/bioinformatics/btz106 | Long-Read, NGS/HTS, Genotype, Polymorphism | Present (Jan 08 2025) | |
| RNA2DSearch | https://doi.org/10.1261/rna.1264109 | RNA Localization, Prediction, Web Server | Absent (Jan 08 2025) | |
| RPT (Repeat Pattern Toolkit) | Repeat Annotation | |||
| RTAnalyzer | https://doi.org/10.1093/nar/gkm313 | LINE1, LINE/Non-LTR Retrotransposon, Homology | Absent (Jan 08 2025) | |
| RTclass1 | https://doi.org/10.1016/j.gene.2009.07.019 | Classification, LINE/Non-LTR Retrotransposon | Present (Jan 08 2025) | |
| RSPB | https://doi.org/10.1093/molbev/msr282 | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Present (Jan 08 2025) | |
| RSVSim | https://doi.org/10.1093/bioinformatics/btt198 | Structural Variation, Simulation | Present (Jan 08 2025) | |
| SalmonTE | https://doi.org/10.1142/9789813235533_0016 | RNA-Seq, Expression, NGS/HTS, Homology | Present (Jan 08 2025) | |
| SAT | https://doi.org/10.1186/1471-2105-8-465 | Simple Sequence Repeat/Microsatellite, Primer, Library Generation, Web Server | Absent (Jan 08 2025) | |
| SatDNA Analyzer | https://doi.org/10.1093/bioinformatics/btm005 | Simple Sequence Repeat/Microsatellite, Alignment, Library Generation | Present (Jan 08 2025) | |
| SATEComp | Link | Homology, Keyword Search, Web Server | Absent (Jan 08 2025) | |
| SciRoKo | https://doi.org/10.1093/bioinformatics/btm157 | Simple Sequence Repeat/Microsatellite, Summary, Annotation | Present (Jan 08 2025) | |
| SCNVSim | https://doi.org/10.1186/s12859-015-0502-7 | CNV/Copy Number Variation, Simulation, Structural Variation | Present (Jan 08 2025) | |
| SCRAMble | https://doi.org/10.1038/s41436-020-0749-x | NGS/HTS, Genotype, Polymorphism, Paired-End | Present (Jan 08 2025) | |
| scTE | https://doi.org/10.1038/s41467-021-21808-x | Single Cell, RNA-Seq, Expression, Eukaryotic Transposon | Present (Jan 08 2025) | |
| SECNVs | https://doi.org/10.3389/fgene.2020.00082 | CNV/Copy Number Variation, Simulation, Expression | Present (Jan 08 2025) | |
| SERpredict | https://doi.org/10.1186/1471-2156-8-78 | RNA-Seq, Expression, Homology | ||
| sideRETRO | https://doi.org/10.1101/2020.03.09.983858 | Pseudogene, CNV/Copy Number Variation, Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| SIGAR | https://doi.org/10.1101/2020.05.05.079426 | NGS/HTS, Short-Read, Split Read | Present (Jan 08 2025) | |
| SIGI-HMM | https://doi.org/10.1186/1471-2105-7-142 | Genomic Island, Codon Usage, HMM | Absent (Jan 08 2025) | |
| Signature.py | https://doi.org/10.1007/978-1-4939-0931-5_12 | Small RNA, piRNA, NGS/HTS | Present (Jan 08 2025) | |
| SimulaTE | https://doi.org/10.1093/bioinformatics/btx772 | Simulation, Genome, NGS/HTS, Genotype, Polymorphism | Present (Jan 08 2025) | |
| SINE-Finder | https://doi.org/10.1105/tpc.111.088682 | SINE, Homology, Motif, Library Generation | Absent (Jan 08 2025) | |
| SINEsFIND | https://doi.org/10.1093/dnares/dsw048 | SINE, Expression, RNA-Seq, NGS/HTS | Present (Jan 08 2025) | |
| SINE_Scan | https://doi.org/10.1093/bioinformatics/btw718 | SINE, Library Generation, Annotation | Present (Jan 08 2025) | |
| SMaRTFinder | Repeat, Annotation | Present (Jan 08 2025) | ||
| SoftSearch | https://doi.org/10.1371/journal.pone.0083356 | Structural Variation, NGS/HTS, Short-Read, Paired-End | ||
| SoftSV | https://doi.org/10.1093/bib/bbv028 | Structural Variation, Paired-End | Present (Jan 08 2025) | |
| SoloTE | https://doi.org/10.1038/s42003-022-04020-5 | RNA-Seq, Expression, Transcription, Single-Cell, NGS/HTS | Present (Jan 08 2025) | |
| sompop | https://doi.org/10.1093/bioinformatics/btaa279 | LINE1, LINE/Non-LTR Retrotransposon, Simulation, Cancer | Present (Jan 08 2025) | |
| somrit | https://www.biorxiv.org/content/10.1101/2023.08.06.552193v2.full.pdf | Retrotransposon, insertion polymorphism, somatic, mosaicism | Present (Jan 08 2025) | |
| SRC (Spark-based RepeatClassifier) | https://doi.org/10.1101/2021.06.03.446998 | RepeatMasker, Classification | Present (Jan 08 2025) | |
| SID (Specific Insertions Detector) | https://doi.org/10.1093/gigascience/gix066 | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (Jan 08 2025) | |
| SPLITREADER | https://doi.org/10.7554/eLife.15716.001 | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (Jan 08 2025) | |
| Sputnik | https://doi.org/10.1038/ng822 | Simple Sequence Repeat/Microsatellite | Absent (Jan 08 2025) | |
| SQUID | https://doi.org/10.1186/s13059-018-1421-5 | RNA-Seq, Expression, NGS/HTS, Structural Variation, Fusion | Present (Jan 08 2025) | |
| SQuIRE | https://doi.org/10.1093/nar/gky1301 | NGS/HTS, RNA-Seq, Expression | Present (Jan 08 2025) | |
| SRF (Satellite Repeat Finder) | https://doi.org/10.1101/gr.278005.123 | Simple Sequence Repeat/Microsatellite, NGS/HTS, Library Generation | Present (Jan 08 2025) | |
| sRNAPipe | https://doi.org/10.1186/s13100-018-0130-7 | Small RNA, RNA-Seq, Annotation | Present (Jan 08 2025) | |
| sRNAplot | https://doi.org/10.1038/s41559-017-0403-4 | Small RNA, piRNA, Visualization | Present (Jan 08 2025) | |
| SRF | https://doi.org/10.1093/bioinformatics/bth103 | Repeat, Web Server | Absent (Jan 08 2025) | |
| SSRIT | Simple Sequence Repeat/Microsatellite, Summary | Present (Jan 08 2025) | ||
| SSRfinder | https://doi.org/10.1023/A:1026346121217 | Simple Sequence Repeat/Microsatellite, EST, Expression | ||
| SSR Locator | http://dx.doi.org/10.1155/2008/412696 | Simple Sequence Repeat/Microsatellite, Primer, PCR, Library Generation | Absent (Jan 08 2025) | |
| SSR Primer | https://doi.org/10.1093/bioinformatics/bth104 | Simple Sequence Repeat/Microsatellite, Primer, Library Generation | Absent (Jan 08 2025) | |
| StainedGlass | https://doi.org/10.1093/bioinformatics/btac018 | Link | Simple Sequence Repeat/Microsatellite, Tandem Repeat, Visualization | Present (Jan 08 2025) |
| STAR | https://doi.org/10.1093/bioinformatics/bth335 | Tandem Repeat, Annotation | Present (Jan 08 2025) | |
| starfish | https://doi.org/10.1101/2023.10.24.563810 | Starship, Tyrosine Recombinase, Detection, Annotation | Present (Jan 08 2025) | |
| STEAK | https://doi.org/10.1093/ve/vex023 | NGS/HTS, Genotype, Polymorphism, Annotation | Present (Jan 08 2025) | |
| STRipy | https://doi.org/10.1101/2021.06.13.448220 | Link | Short Tandem Repeat, Genotype, NGS/HTS | Present (Jan 08 2025) |
| STRling | https://doi.org/10.1186/s13059-022-02826-4 | Short Tandem Repeat, Annotation, NGS/HTS | Present (Jan 08 2025) | |
| SURVIVOR | https://doi.org/10.1038/ncomms14061 | Structural Variation, NGS/HTS, Simulation | Present (Jan 08 2025) | |
| SV2 | https://doi.org/10.1093/bioinformatics/btx813 | Structural Variation, Machine Learning, Paired-End | Present (Jan 08 2025) | |
| svaRetro | https://doi.org/10.46471/gigabyte.70 | Structural Variation, Pseudogene, Expression, Transcription, LINE/Non-LTR Retrotransposon | Present (Jan 08 2025) | |
| SV-AUTOPILOT | https://doi.org/10.1186/s12864-015-1376-9 | Structural Variation, Benchmarking | ||
| SV-Bay | https://doi.org/10.1093/bioinformatics/btv751 | Structural Variation, NGS/HTS, Bayesian | Present (Jan 08 2025) | |
| svclassify | https://doi.org/10.1186/s12864-016-2366-2 | Structural Variation, Clustering, Classification | Present (Jan 08 2025) | |
| SVDetect | https://doi.org/10.1093/bioinformatics/btq293 | NGS/HTS, Structural Variation, Paired-End | Present (Jan 08 2025) | |
| SVDSS | NGS/HTS, Structural Variation, Long-Read | Present (Jan 08 2025) | ||
| SVEngine | https://doi.org/10.1093/gigascience/giy081 | Structural Variation, Simulation | Present (Jan 08 2025) | |
| SVelter | https://doi.org/10.1186/s13059-016-0993-1 | Structural Variation, NGS/HTS | Present (Jan 08 2025) | |
| SVIM | https://doi.org/10.1093/bioinformatics/btz041 | NGS/HTS, Long-Read, Structural Variation | Present (Jan 08 2025) | |
| SVM2 | https://doi.org/10.1093/nar/gks606 | Structural Variation, Supervised Learning | ||
| SVmine | https://doi.org/10.1093/bioinformatics/btx455 | Structural Variation, Pipeline | Present (Jan 08 2025) | |
| SVPV | https://doi.org/10.1093/bioinformatics/btx117 | Structural Variation, Visualization | Present (Jan 08 2025) | |
| svviz2 | https://doi.org/10.1093/bioinformatics/btv478 | Structural Variation, Visualization | Present (Jan 08 2025) | |
| SVXplorer | https://doi.org/10.1371/journal.pcbi.1007737 | NGS/HTS, Paired-End, Structural Variation | Present (Jan 08 2025) | |
| SWGIS v2.0 | https://doi.org/10.1186/s12864-018-4724-8 | Genomic Island, Eukaryote, K-mer | Present (Jan 08 2025) | |
| SyRI | https://doi.org/10.1186/s13059-019-1911-0 | Structural Variation, NGS/HTS, Comparative, Whole Genome | Present (Jan 08 2025) | |
| T3E | https://doi.org/10.1186/s13100-022-00285-z | ChIP-Seq, NGS/HTS | Present (Jan 08 2025) | |
| TandemTools | https://doi.org/10.1093/bioinformatics/btaa440 | Tandem Repeat, Long-Read, NGS/HTS, Assembly Polishing, Read Mapping | Present (Jan 08 2025) | |
| Tandem Repeat Annotation Library | https://doi.org/10.1093/bioinformatics/btv306 | Tandem Repeat, Annotation | Present (Jan 08 2025) | |
| Tallymer | https://doi.org/10.1186/1471-2164-9-517 | K-mer Counting | Present (Jan 08 2025) | |
| TANGRAM | https://doi.org/10.1186/1471-2164-15-795 | Polymorphism, Genotype, NGS/HTS | Present (Jan 08 2025) | |
| tantan | https://doi.org/10.1093/nar/gkq1212 | Repeat, Repeat Masking | Absent (Jan 08 2025) | |
| TAPDANCE | https://doi.org/10.1186/1471-2105-13-154 | Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| TAPO | https://doi.org/10.1016/j.febslet.2015.08.025 | Tandem Repeat, Web Server | Present (Jan 08 2025) | |
| TARDIS | http://dx.doi.org/10.1016/j.ymeth.2017.05.030 | Structural Variation, NGS/HTS | Present (Jan 08 2025) | |
| TARGeT (Tree Analysis of Related Genes and Transposons) | https://doi.org/10.1093/nar/gkp295 | Homology, Web Server | Present (Jan 08 2025) | |
| TASR | https://doi.org/10.1093/nar/gkv257 | Small RNA, Annotation | Present (Jan 08 2025) | |
| TCF | https://doi.org/10.1371/journal.pcbi.0030137 | Nested Insertion, Annotation, Web Server | Absent (Jan 08 2025) | |
| TEBreak | https://doi.org/10.1186/s13100-016-0076-6 | Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| TECDetec | https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.718854 | Expression, Transcription, Chimera, NGS/HTS | Present (Jan 08 2025) | |
| TECookbook | https://doi.org/10.1093/nargab/lqad078 | Chip-Seq, NGS/HTS, Analysis | Present (Jan 08 2025) | |
| TE-Aid | https://doi.org/10.1186/s13100-021-00259-7 | Annotation, Classification, Manual Curation, TE Libraries QC | Present (Jan 08 2025) | |
| TE_Density | https://doi.org/10.1186/s13100-022-00264-4 | Annotation, Analysis | Present (Jan 08 2025) | |
| TE Displayer | https://doi.org/10.1093/bioinformatics/btq639 | TE Display | Absent (Jan 08 2025) | |
| TEffectR | https://doi.org/10.7717/peerj.8192 | RNA-Seq, Expression, NGS/HTS, Homology, Annotation | Present (Jan 08 2025) | |
| TE transcripts | https://doi.org/10.1093/bioinformatics/btv422 | Expression, Transcription, RNA-Seq | Present (Jan 08 2025) | |
| TE (Insertion/Deletion Dynamics for Transposable Elements) | https://doi.org/10.1534/genetics.118.301198 | Indel, Insertion Time, LTR Retrotransposon, Aegilops | Present (Jan 08 2025) | |
| TE_Discovery | https://doi.org/10.1101/701888 | Homology, Library Generation, Annotation, Analysis | Present (Jan 08 2025) | |
| TEA | https://doi.org/10.1126/science.1222077 | Genotype, Polymorphism | Present (Jan 08 2025) | |
| TEcandidates | https://doi.org/10.1093/bioinformatics/bty423 | Expression, Transcription, RNA-Seq | Present (Jan 08 2025) | |
| TEclass | https://doi.org/10.1093/bioinformatics/btp084 | Classification | Present (Jan 08 2025) | |
| TEclass2 | https://doi.org/10.1101/2023.10.13.562246 | Classification, Webserver | Present (Jan 08 2025) | |
| Tedna | https://doi.org/10.1093/bioinformatics/btu365 | Assembly, Illumina, Paired-End, NGS/HTS | Present (Jan 08 2025) | |
| TEF (Transposable Element Finder) | https://doi.org/10.1186/s12859-022-05011-3 | Polymorphism, Genotype, NGS/HTS | Present (Jan 08 2025) | |
| TEfinder | https://doi.org/10.3390/genes12020224 | Polymorphism, Genotype, NGS/HTS | Present (Jan 08 2025) | |
| TEFLoN | https://doi.org/10.1093/gbe/evx050 | Annotation, Classification, NGS/HTS, Polymorphism, Genotype, Paired-End, Illumina | Present (Jan 08 2025) | |
| TE-greedy-nester | https://doi.org/10.1093/bioinformatics/btaa632 | Link | Nested Insertion, LTR Retrotransposon | Present (Jan 08 2025) |
| TEGRiP | https://doi.org/10.1101/2021.02.25.432867 | Eukaryotic Transposon, Annotation, Gene | Present (Jan 08 2025) | |
| TE-invasion-simulations | https://doi.org/10.1093/gbe/evy218 | Simulation, Genome, Evolution | Present (Jan 08 2025) | |
| tek2 | https://doi.org/10.1093/molbev/msz220 | Simulation, Genome, Divergence, Evolution | Present (Jan 08 2025) | |
| TE-Learner | https://doi.org/10.1371/journal.pcbi.1006097 | Machine Learning, LTR Retrotransposon, Classification | Absent (Jan 08 2025) | |
| Telescope | https://doi.org/10.1371/journal.pcbi.1006453 | Expression, Transcription, RNA-Seq | Present (Jan 08 2025) | |
| TElocal | Expression, Transcription, RNA-Seq | Present (Jan 08 2025) | ||
| TE-locate | https://doi.org/10.3390/biology1020395 | NGS/HTS, Paired-End, Genotype, Polymorphism | Present (Jan 08 2025) | |
| TELR | NGS/HTS, PacBio, Oxford Nanopore, Long-Read, Genotype, Polymorphism | Present (Jan 08 2025) | ||
| TEmarker | https://doi.org/10.1016/j.xplc.2021.100270 | Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| TEMP | https://doi.org/10.1093/nar/gku323 | Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| TEMP2 | https://doi.org/10.1093/nar/gkab010 | Genotype, Polymorphism, NGS/HTS, Short-Read | Present (Jan 08 2025) | |
| TE-nester | https://ieeexplore.ieee.org/document/8621071 | Structure, Nested Insertion | Present (Jan 08 2025) | |
| TEnest | https://doi.org/10.1104/pp.107.110353 | Nested Insertion, Annotation | ||
| TEnest 2.0 | https://doi.org/10.1007/978-1-62703-568-2_22 | Nested Insertion, Annotation | Present (Jan 08 2025) | |
| TEPEAK | https://doi.org/10.1101/2023.10.13.562297 | Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| TEpeaks | ChIP-Seq | Present (Jan 08 2025) | ||
| tephra | Homology, Library Generation, Structure, Classification, Age, Annotation | Present (Jan 08 2025) | ||
| TEPID | https://doi.org/10.7554/eLife.20777.001 | Polymorphism, Genotype, NGS/HTS | Present (Jan 08 2025) | |
| TE-reX | https://doi.org/10.1101/2020.07.02.163816 | Genotype, Polymorphism, Recombination | Present (Jan 08 2025) | |
| TERAD | https://doi.org/10.1111/1755-0998.13080 | RAD-Seq, Repeat Masking, Annotation | Present (Jan 08 2025) | |
| TERL | https://doi.org/10.1093/bib/bbaa185 | Classification, Neural Network | Present (Jan 08 2025) | |
| TESD | https://doi.org/10.1093/bioinformatics/btl454 | Simulation, Genome | Absent (Jan 08 2025) | |
| TESeeker | https://doi.org/10.1186/1471-2105-12-130 | Homology, VirtualBox, Library Generation | Absent (Jan 08 2025) | |
| TEsmall | https://doi.org/10.3389/fgene.2018.00461 | NGS/HTS, Small RNA, piRNA, Annotation | Present (Jan 08 2025) | |
| TEsorter | https://doi.org/10.1093/hr/uhac017 | Link | Classification, HMM | Present (Jan 08 2025) |
| TEspeX | https://doi.org/10.1093/bioinformatics/btac526 | Zenodo | NGS/HTS, Abundance, Expression, Transcription | Present (Jan 08 2025) |
| TE-Tracker | https://doi.org/10.1186/s12859-014-0377-z | Polymorphism, Genotype | Present (Jan 08 2025) | |
| TETyper | https://doi.org/10.1099/mgen.0.000232 | Short-Read, Paired-End, Polymorphism, Genotype, Archaea, Bacteria | Present (Jan 08 2025) | |
| TeXP | https://doi.org/10.1371/journal.pcbi.1007293 | Expression, Transcription, RNA-Seq, NGS/HTS, LINE/Non-LTR Retrotransposon, Activity, Short-Read | Present (Jan 08 2025) | |
| The RIPper | https://doi.org/10.7717/peerj.7447 | Link | RIP/Repeat-Induced Point Mutation, Mutation, GC, Repeat, Web Server | Present (Jan 08 2025) |
| TIDAL | https://doi.org/10.1093/nar/gkv1193 | Genotype, Polymorphism, Illumina, Drosophila | Present (Jan 08 2025) | |
| TIDDIT | https://f1000research.com/articles/6-664/v2 | Rearrangement, NGS/HTS, Structural Variation | Present (Jan 08 2025) | |
| TideHunter | https://doi.org/10.1093/bioinformatics/btz376 | Long-Read, Tandem Repeat, NGS/HTS | Present (Jan 08 2025) | |
| TIDK (Telomere Identifcation toolKit) | Github | De Novo, Telomere, Visualization | Present (Jan 08 2025) | |
| TIGER (Target Integrative Genetic Element Retriever) | https://doi.org/10.1093/nar/gkaa156 | ICE/Integrative and Conjugative Element, Prophage/Bacteriophage | Present (Jan 08 2025) | |
| Tinscan | Comparative, Polymorphism, Genotype | Present (Jan 08 2025) | ||
| TinT (Transposition in Transposition) | https://doi.org/10.1186/1471-2148-10-376 | Nested Insertion, Web Server | Present (Jan 08 2025) | |
| TIF (Transposon Insertion Finder) | https://doi.org/10.1186/1471-2105-15-71 | NGS/HTS, Genotype, Polymorphism, Short-Read | Present (Jan 08 2025) | |
| TIP_finder | https://doi.org/10.3390/biology9090281 | NGS/HTS, Genotype, Polymorphism | Present (Jan 08 2025) | |
| TIPseq-Hunter | https://doi.org/10.1073/pnas.1619797114 | Paired-End, Illumina, Machine Learning | Present (Jan 08 2025) | |
| TIR-Finder | https://doi.org/10.4137/EBO.S10619 | ITR/TIR/DNA Transposon, Web Server, Homology, Structure | Present (Jan 08 2025) | |
| TIR-Learner | https://doi.org/10.1016/j.molp.2019.02.008 | ITR/TIR/DNA Transposon, Homology, Structure, Annotation | Present (Jan 08 2025) | |
| TIRMITE | MITE, HMM, ITR/TIR/DNA Transposon, Annotation | Present (Jan 08 2025) | ||
| T-lex | https://doi.org/10.1093/nar/gkq1291 | Genotype, Polymorphism, NGS/HTS | Absent (Jan 08 2025) | |
| T-lex2 | https://doi.org/10.1093/nar/gku1250 | Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| T-lex3 | https://doi.org/10.1093/bioinformatics/btz727 | Genotype, Polymorphism, NGS/HTS | Present (Jan 08 2025) | |
| TLDR | https://doi.org/10.1101/2020.05.24.113068 | NGS/HTS, Long-Read, Genotype, Polymorphism | ||
| TnComp_finder | Composite Transposon | Absent (Jan 08 2025) | ||
| Tn3_finder | https://doi.org/10.1128/mBio.00452-20 | Transposon | Absent (Jan 08 2025) | |
| Tn3+TA_finder | https://doi.org/10.1128/mBio.00452-20 | Transposon, Toxin-Antitoxin Loci | Present (Jan 08 2025) | |
| Tn-Core | https://doi.org/10.1021/acssynbio.8b00432 | Tn-Seq, Transposon Mutagenesis, RNA-Seq, Metabolic Modelling | Present (Jan 08 2025) | |
| TnPred | http://dx.doi.org/10.1155/2012/678761 | Web Server, Transposase, Archaea, Bacteria, IS Element | Present (Jan 08 2025) | |
| Tn-seq Explorer | https://doi.org/10.1371/journal.pone.0126070 | Tn-Seq, Transposon Mutagenesis | Present (Jan 08 2025) | |
| TRACKPOSON | https://doi.org/10.1038/s41467-018-07974-5 | Genotype, Polymorphism, Paired-End, NGS/HTS | Absent (Jan 08 2025) | |
| TraDIS toolkit | https://doi.org/10.1093/bioinformatics/btw022 | Tn-Seq, Transposon Mutagenesis | Present (Jan 08 2025) | |
| TraFIC | https://doi.org/10.1126/science.1251343 | NGS/HTS, Paired-End, Homo sapiens, Genotype, Polymorphism | Present (Jan 08 2025) | |
| TRANScendence | https://doi.org/10.1186/s12859-017-1824-4 | De Novo, Homology, Structure, Library Generation, Annotation, Web Server | Present (Jan 08 2025) | |
| TRANSIT | https://doi.org/10.1371/journal.pcbi.1004401 | Tn-Seq, Transposon Mutagenesis | Present (Jan 08 2025) | |
| TRANSPO | ITR/TIR/DNA Transposon, Homology | Absent (Jan 08 2025) | ||
| TranspoScope | https://doi.org/10.1093/bioinformatics/btaa244 | Genotype, Polymorphism, Visualization, NGS/HTS | Present (Jan 08 2025) | |
| Transposeq | https://doi.org/10.1101/gr.163659.113 | Polymorphism, Genotype, Web Server, Homo sapiens, Eukaryotic Retrotransposon | Absent (Jan 08 2025) | |
| Transposome | https://doi.org/10.1093/bioinformatics/btv059 | De Novo, Assembly, Homology | Present (Jan 08 2025) | |
| Transposon Cluster Finder | https://doi.org/10.1371/journal.pcbi.0030137 | Nested Insertion | Absent (Jan 08 2025) | |
| TransposonPSI | BLAST, Eukaryotic Transposon | Present (Jan 08 2025) | ||
| TransposonUltimate | https://doi.org/10.1093/nar/gkac136 | Link | Eukaryotic Transposon, Library Generation, Classification, Annotation, Structural Variation | Present (Jan 08 2025) |
| TranSurVeyor | https://doi.org/10.1093/nar/gky685 | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (Jan 08 2025) | |
| TRAP | https://doi.org/10.1093/bioinformatics/bti809 | Tandem Repeat | ||
| TRASH (Tandem Repeat Annotation and Structural Hierarchy) | https://doi.org/10.1093/bioinformatics/btad308 | Tandem Repeat, Annotation, K-mer | Present (Jan 08 2025) | |
| T-REKS | https://doi.org/10.1093/bioinformatics/btp482 | Tandem Repeat | Present (Jan 08 2025) | |
| TRcaller | https://doi.org/10.1101/2023.02.15.528687 | Tandem Repeat, NGS/HTS, Long-Read, Short-Read | Absent (Jan 08 2025) | |
| TrEMOLO | https://doi.org/10.1101/2022.07.21.500944 | NGS/HTS, Long-Read, Oxford Nanopore, Genotype, Polymorphism | Present (Jan 08 2025) | |
| TRF | https://doi.org/10.1093/nar/27.2.573 | Tandem Repeat | Present (Jan 08 2025) | |
| TRGT (Tandem Repeat Genotyping Tool) | https://doi.org/10.1101/2023.05.12.540470 | Tandem Repeat, PacBio, Long-Read, NGS/HTS, Genotype | Present (Jan 08 2025) | |
| TRiCoLOR | https://doi.org/10.1093/gigascience/giaa101 | Tandem Repeat, NGS/HTS, Long-Read | Present (Jan 08 2025) | |
| tRNAscan-SE- On-line | https://doi.org/10.1093/nar/gkw413 | Link | tRNA | Absent (Jan 08 2025) |
| tRNA-DL | https://doi.org/10.1159/000493215 | tRNA, Deep Neural Network | ||
| TROLL | https://doi.org/10.1093/bioinformatics/18.4.634 | Tandem Repeat | Present (Jan 08 2025) | |
| TRTools | https://doi.org/10.1101/2020.03.17.996033 | Tandem Repeat, Genotype | Present (Jan 08 2025) | |
| TrustTEr | https://doi.org/10.1101/2020.07.07.191668 | RNA-Seq, Expression | ||
| TSDFinder | https://doi.org/10.1186/gb-2002-3-10-research0052 | LINE1, LINE/Non-LTR Retrotransposon, Target Site Duplication | Absent (Jan 08 2025) | |
| TypeTE | https://doi.org/10.1093/nar/gkaa074 | Genotype, Polymorphism | Present (Jan 08 2025) | |
| UCSC Repeat Browser | https://doi.org/10.1101/429613 | Repeat, Visualization, Annotation | Present (Jan 08 2025) | |
| ULTRA | https://doi.org/10.1145/3233547.3233604 | Tandem Repeat, HMM, Repeat Masking | Present (Jan 08 2025) | |
| V-ELMpiRNAPred | https://doi.org/10.1142/S0219720016500463 | piRNA, Neural Network | Absent (Jan 08 2025) | |
| VariationHunter | https://doi.org/10.1093/bioinformatics/btq216 | NGS/HTS, Genotype, Polymorphism, Homo sapiens | ||
| VHICA | https://doi.org/10.1093/molbev/msv341 | Horizontal Transfer | Present (Jan 08 2025) | |
| VirSorter | https://doi.org/10.7717/peerj.985 | Prophage/Bacteriophage, Homology, HMM | Present (Jan 08 2025) | |
| VirusSeq | https://doi.org/10.1093/bioinformatics/bts665 | Virus, RNA-Seq, Homo sapiens | Present (Jan 08 2025) | |
| VirusTaxo | https://doi.org/10.1101/2021.04.29.442004 | Virus, K-mer, Classification, Web Server | Present (Jan 08 2025) | |
| VISMapper | https://doi.org/10.1186/s12859-017-1837-z | Virus, NGS/HTS, Web Server, Genotype, Polymorphism, Insertion Site, Visualization | Present (Jan 08 2025) | |
| VisualTE | https://doi.org/10.1186/s12864-015-1351-5 | Annotation, Visualization | ||
| VisualRepbase | https://doi.org/10.1186/1471-2105-9-345 | Annotation, Visualization | Present (Jan 08 2025) | |
| vHULK (Viral Host UnveiLing Kit) | https://doi.org/10.1101/2020.12.06.413476 | Prophage/Bacteriophage | Present (Jan 08 2025) | |
| Vmatch | Repeat Annotation | Present (Jan 08 2025) | ||
| VRprofile | https://doi.org/10.1093/bib/bbw141 | Virulence, AMR/Antibiotic Resistance | Present (Jan 08 2025) | |
| VRprofile2 | https://doi.org/10.1093/nar/gkac321 | Virulence, AMR/Antibiotic Resistance | Present (Jan 08 2025) | |
| WGSSAT | https://doi.org/10.1093/jhered/esx075 | Simple Sequence Repeat/Microsatellite, Repeat Annotation, Primer | Present (Jan 08 2025) | |
| WtP (What the Phage) | https://doi.org/10.1101/2020.07.24.219899 | Prophage/Bacteriophage, Annotation, Classification, Pipeline | Present (Jan 08 2025) | |
| WindowMasker | https://doi.org/10.1093/bioinformatics/bti774 | Repeat Masking, Annotation, De Novo | Present (Jan 08 2025) | |
| Winnowmap2 | https://doi.org/10.1101/2020.11.01.363887 | Long-Read, NGS/HTS, Repeat | Present (Jan 08 2025) | |
| xenoGI | https://doi.org/10.1186/s12859-018-2038-0 | Genomic Island, Synteny, Phylogeny | Present (Jan 08 2025) | |
| xTea | https://doi.org/10.1038/s41467-021-24041-8 | Eukaryotic Transposon, Polymorphism, Genotype, Long-Read, Short-Read, Pangenome | Present (Jan 08 2025) | |
| YASS | https://doi.org/10.1093/nar/gki478 | Dot Plot, Visualization, Alignment, Web Server | Absent (Jan 08 2025) | |
| YORO | https://doi.org/10.1371/journal.pone.0291925 | Classification, LTR Retrotransposon, Convolutional Neural Network | Present (Jan 08 2025) | |
| Zisland Explorer | https://doi.org/10.1093/bib/bbw019 | Genomic Island, GC | Absent (Jan 08 2025) |