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 |
|---|---|---|---|---|
| 2-n-way Genome Suite | https://doi.org/10.1101/gr.262261.120 | Polymorphism, Genotype, Web Server | Present (May 01 2026) | |
| 2lpiRNApred | https://doi.org/10.1080/15476286.2020.1734382 | piRNA | Present (May 01 2026) | |
| 4-LIN | https://doi.org/10.1093/sysbio/syac082 | Web Server, Phylogeny, Eukaryotic Retrotransposon | Present (May 01 2026) | |
| AAARF (Assisted Automated Assembler of Repeat Families) | https://doi.org/10.1186/1471-2105-9-235 | Homology, Alignment | Present (May 01 2026) | |
| ANUBIS | https://doi.org/10.1093/nar/gkaa679 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism, Visualization | Present (May 01 2026) | |
| ARTIST | https://doi.org/10.1371/journal.pgen.1004782 | Tn-Seq, Transposon Mutagenesis, HMM | Present (May 01 2026) | |
| AgIn | https://doi.org/10.1093/bioinformatics/btw360 | PacBio, Methylation | Present (May 01 2026) | |
| AlbaTraDIS | https://doi.org/10.1371/journal.pcbi.1007980 | Tn-Seq, Transposon Mutagenesis | Present (May 01 2026) | |
| Alien_Hunter | https://doi.org/10.1093/bioinformatics/btl369 | Genomic Island, HMM | Absent (May 01 2026) | |
| Alpha-CENTAURI | https://doi.org/10.1093/bioinformatics/btw101 | Satellite, Centromere, Tandem Repeat, HMM, Long Read | Present (May 01 2026) | |
| AluMine | https://doi.org/10.1101/588434 | Alu, SINE, Genotype, Polymorphism, NGS/HTS | Present (May 01 2026) | |
| AnTE | https://doi.org/10.1371/journal.pgen.1004482 | Simulation, Phylogeny, Bayesian MCMC, Ancestral Reconstruction | Absent (May 01 2026) | |
| AnnoSINE | https://doi.org/10.1093/plphys/kiab524 | SINE, Annotation, HMM | Present (May 01 2026) | |
| AntiDefenseFinder | https://doi.org/10.1093/nar/gkae1171 | Link | Web Server, Anti-Defense System, Bacteria, Archaea, Prophage/Bacteriophage | Present (May 01 2026) |
| Attacca | https://doi.org/10.1186/1471-2105-10-281 | Integron | ||
| BERTE | https://doi.org/10.1101/2024.01.28.577612 | Classification | Present (May 01 2026) | |
| BLATCAT | https://doi.org/10.1155/2014/730814 | BLAT, Homology | ||
| 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 (May 01 2026) | |
| BacAnt | https://doi.org/10.3389/fmicb.2021.649969 | Link | IS Element, Archaeal/Bacterial Transposon, Integron, AMR/Antibiotic Resistance, Annotation, Web Server | Absent (May 01 2026) |
| Bakta | https://doi.org/10.1099/mgen.0.000685 | Link | Metagenomics, Annotation | Present (May 01 2026) |
| Bellerophon | https://doi.org/10.1186/1471-2105-14-s5-s6 | Structural Variation, NGS/HTS, Paired-End | ||
| BreakDancer | https://doi.org/10.1038/nmeth.1363 | Structural Variation, NGS/HTS, Short Read, Paired-End, MAQ | Absent (May 01 2026) | |
| CAFE (Coefficient-based Analysis of Fitness by read Enrichments) | https://doi.org/10.1093/bioinformatics/btaa1086 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (May 01 2026) | |
| CARP | https://doi.org/10.1371/journal.pone.0193588 | De Novo, Library Generation, Homology, Annotation | Present (May 01 2026) | |
| CAULIFINDER | https://doi.org/10.1186/s13100-022-00288-w | Detection, Annotation, EVE/Endogenous Viral Element, Plants, Virus | Present (May 01 2026) | |
| CAlu Alu Classifier | https://doi.org/10.1016/j.cell.2010.05.020 | Genotype, Polymorphism, Homo sapiens, Alu, SINE, Web Server | Absent (May 01 2026) | |
| CELLO-Seq (single CELl LOng read RNA sequencing) | https://doi.org/10.1101/2020.10.02.322073 | Single-Cell, RNA-Seq, Eukaryotic Transposon | Present (May 01 2026) | |
| CGS | https://doi.org/10.1186/1471-2164-13-245 | Horizontal Transfer, K-mer | ||
| CIAlign | https://doi.org/10.7717/peerj.12983 | Alignment, MSA, Manual Curation | Present (May 01 2026) | |
| CLARI-TE | https://doi.org/10.1186/s13059-014-0546-4 | Homology, Annotation, Nested Insertion | Present (May 01 2026) | |
| CLIFinder | https://doi.org/10.1093/bioinformatics/btx671 | LINE1, Transcription, RNA-Seq, Expression, Chimera, NGS/HTS | Present (May 01 2026) | |
| CLOVE | https://doi.org/10.1186/s12859-017-1760-3 | Structural Variation | Present (May 01 2026) | |
| ColabCuraTE | https://doi.org/10.1186/s13100-025-00389-2 | Manual Curation | Present (May 01 2026) | |
| COLOMBO | https://doi.org/10.1186/1471-2105-7-142 | Genomic Island, Codon Usage, HMM | Present (May 01 2026) | |
| CONJscan | https://doi.org/10.1007/978-1-4939-9877-7_19 | Plasmid, ICE/Integrative and Conjugative Element | Present (May 01 2026) | |
| COPLA | https://doi.org/10.1101/2020.12.15.422809 | Plasmid, Classification, Homology | Present (May 01 2026) | |
| COSEG | Subfamily Identification, Eukaryotic Transposon, Alu, SINE | Present (May 01 2026) | ||
| CRISPRCasTyper | https://doi.org/10.1101/2020.05.15.097824 | Link | CRISPR, Classification, Annotation | Present (May 01 2026) |
| Censor | https://doi.org/10.1016/S0097-8485(96)80013-1 | Annotation, Repeat Masking | Present (May 01 2026) | |
| ChimeraTE | https://doi.org/10.1093/nar/gkad671 | RNA-Seq, Expression, Transcription, Paired-End, NGS/HTS, Chimera | Present (May 01 2026) | |
| ClassifyTE | https://doi.org/10.1093/bioinformatics/btab146 | Classification, Eukaryotic Transposon | Present (May 01 2026) | |
| ClustAGE | https://doi.org/10.1186/s12859-018-2154-x | Comparative, BLAST, Archaea, Bacteria | Present (May 01 2026) | |
| CompTIS | https://doi.org/10.1128/mSphere.00031-19 | Tn-Seq, Transposon Mutagenesis, PCA | Present (May 01 2026) | |
| ConTExt | https://genome.cshlp.org/content/28/5/714 | Illumina, Paired-End, Homology, NGS/HTS, Polymorphism | Present (May 01 2026) | |
| ConsensuSV | https://doi.org/10.1093/bioinformatics/btac709 | Structural Variation, Pipeline, Indel, Polymorphism | Present (May 01 2026) | |
| ConsensusSV | https://doi.org/10.1093/bioinformatics/btac709 | NGS/HTS, Short Read, Illumina, Structural Variation | Present (May 01 2026) | |
| D-Genies | https://doi.org/10.7717/peerj.4958 | Dot Plot, Visualization | Present (May 01 2026) | |
| DANTE | Link | Homology, Library Generation | Present (May 01 2026) | |
| 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 (May 01 2026) | |
| DARTS (Domain-Associated RetroTransposon Search) | https://doi.org/10.1101/2021.12.03.471067 | Pipeline, Homology, Annotation, Retrotransposon | Present (May 01 2026) | |
| DAWG-PAWS | https://doi.org/10.1186/1746-4811-5-8 | Homology, HMM, Annotation, Gene Prediction | Present (May 01 2026) | |
| DBSCAN-SWA | https://doi.org/10.1101/2020.07.12.199018 | Prophage/Bacteriophage, Homology | Present (May 01 2026) | |
| DD-Detection | https://doi.org/10.1093/bioinformatics/btv621 | NGS/HTS, Illumina, Paired-End, Polymorphism | Present (May 01 2026) | |
| DEPht | https://doi.org/10.1093/nar/gkac273 | Annotation, Extraction, Prophage/Bacteriophage | Present (May 01 2026) | |
| DGRscan | https://doi.org/10.3390/ijms150814234 | DGR/Diversity Generating Retroelement, Annotation | Present (May 01 2026) | |
| DIVE | https://doi.org/10.1101/2022.06.13.495703 | De Novo, K-mer, Repeat | Present (May 01 2026) | |
| DTExpress | https://doi.org/10.1007/978-1-0716-1134-0_2 | RNA-Seq, Expression | Present (May 01 2026) | |
| DarkHorse | https://doi.org/10.1186/gb-2007-8-2-r16 | Horizontal Transfer, Homology, Phylogeny | Present (May 01 2026) | |
| DeBreak | https://doi.org/10.21203/rs.3.rs-1261915/v1 | NGS/HTS, Long Read, Structural Variation | Present (May 01 2026) | |
| DeRIP | https://doi.org/10.1186/1471-2164-11-655 | RIP/Repeat-Induced Point Mutation, Prediction, Fungi | Present (May 01 2026) | |
| DeepMEI | https://doi.org/10.1101/2023.03.07.531451 | NGS/HTS, Short Read, Genotype, Polymorphism, Convolutional Neural Network | Present (May 01 2026) | |
| DeepRepeat | https://doi.org/10.1186/s13059-022-02670-6 | NGS/HTS, Short Tandem Repeat, Long Read, Oxford Nanopore | Present (May 01 2026) | |
| DeepTE | https://doi.org/10.1093/bioinformatics/btaa519 | Classification, Convolutional Neural Network | Present (May 01 2026) | |
| Delly | https://doi.org/10.1093/bioinformatics/bts378 | Structural Variation, NGS/HTS, Short Read, Paired-End | Present (May 01 2026) | |
| Design-Island | https://doi.org/10.1186/1471-2164-9-150 | Genomic Island, Monte-Carlo, GC, Codon Usage | ||
| DeviaTE | https://doi.org/10.1111/1755-0998.13030 | NGS/HTS, Abundance, Visualization, Divergence | Present (May 01 2026) | |
| DiGReF | https://doi.org/10.1186/1471-2164-13-430 | DGR/Diversity Generating Retroelement, Annotation | Absent (May 01 2026) | |
| Dna-brnn | https://doi.org/10.1093/bioinformatics/btz264 | Satellite, Centromere, Neural Network | Present (May 01 2026) | |
| Domain Organizer | https://doi.org/10.1093/bioinformatics/btl337 | Alignment, HMM, Domain, Visualization | Absent (May 01 2026) | |
| Dotlet | https://doi.org/10.1093/bioinformatics/16.2.178 | Dot Plot, Visualization | Present (May 01 2026) | |
| Dotter | https://doi.org/10.1016/0378-1119(95)00714-8 | Visualization, Dot Plot | Present (May 01 2026) | |
| Duster | https://peercommunityjournal.org/articles/10.24072/pcjournal.68/ | Library Generation, Homology, K-mer | Present (May 01 2026) | |
| Dysgu | https://doi.org/10.1093/nar/gkac039 | NGS/HTS, Short Read, Long Read, Structural Variation | Present (May 01 2026) | |
| EAHelitron | https://doi.org/10.1186/s12859-019-2945-8 | Helitron, Structure | Present (May 01 2026) | |
| ECCsplorer | https://doi.org/10.1186/s12859-021-04545-2 | eccDNA, Identification, Active TEs | Present (May 01 2026) | |
| EDTA | https://doi.org/10.1186/s13059-019-1905-y | Library Generation, Filtering, Structure, De Novo | Present (May 01 2026) | |
| EGID | https://doi.org/10.6026/007/97320630007311 | Genomic Island, Prediction | Absent (May 01 2026) | |
| ELAN | https://doi.org/10.1093/nar/gkr337 | Homology, Insertion Site, Consensus | Absent (May 01 2026) | |
| ELITE (Efficiently Locating Insertions of Transposable Elements) | https://doi.org/10.1145/3307339.3342182 | Genotype, Polymorphism, NGS/HTS | Absent (May 01 2026) | |
| ERVcaller | https://doi.org/10.1093/bioinformatics/btz205 | ERV/Endogenous Retrovirus, Homo sapiens, NGS/HTS, Polymorphism, Genotype | Absent (May 01 2026) | |
| ERVmap | https://doi.org/10.1073/pnas.1814589115 | ERV/Endogenous Retrovirus, RNA-Seq, Transcriptome, Homo sapiens | Present (May 01 2026) | |
| ESAP Plus | https://doi.org/10.1186/s12864-016-3328-4 | Simple Sequence Repeat/Microsatellite, Expression, EST, Clustering, Repeat Masking | Absent (May 01 2026) | |
| ESMP | https://doi.org/10.6026/97320630008206 | Simple Sequence Repeat/Microsatellite, Expression, EST, Clustering | Absent (May 01 2026) | |
| ESSENTIALS | https://doi.org/10.1371/journal.pone.0043012 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Absent (May 01 2026) | |
| EVANGELIST | https://doi.org/10.3390/genes12020312 | GC, Repeat Annotation | Present (May 01 2026) | |
| EarlGrey | https://doi.org/10.21203/rs.3.rs-1812599/v1 | Pipeline, Annotation, Repeat Masking, Homology, De Novo, Library Generation | Present (May 01 2026) | |
| Easymap | https://doi.org/10.3389/fpls.2021.655286 | Link | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (May 01 2026) |
| Ecc_finder | https://www.frontiersin.org/articles/10.3389/fpls.2021.743742/abstract | essDNA, NGS/HTS, Oxford Nanopore | Present (May 01 2026) | |
| EpiTEome | https://doi.org/10.1186/s13059-017-1232-0 | Polymorphism, Genotype, NGS/HTS, Methyl-Seq, Bisulfite, Methylation, | Present (May 01 2026) | |
| ExoPLOT | https://doi.org/10.1016/j.ygeno.2022.110434 | RNA-Seq, Expression, Transcription, NGS/HTS | Present (May 01 2026) | |
| ExpansionHunter | https://doi.org/10.1101/gr.225672.117 | Short Read, NGS/HTS, Short Tandem Repeat | Present (May 01 2026) | |
| ExpansionHunter Denovo | https://doi.org/10.1101/863035 | Short Read, NGS/HTS, Short Tandem Repeat | Present (May 01 2026) | |
| ExplorATE | https://doi.org/10.1093/bioinformatics/btac354 | Expression, Transcription, RNA-Seq | Present (May 01 2026) | |
| FASTQINS | https://doi.org/10.1093/nar/gkaa679 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism, Read Mapping | Present (May 01 2026) | |
| FORRepeats | https://doi.org/10.1093/bioinformatics/btf843 | Repeat, Detection | ||
| FasTE | https://doi.org/10.1111/1755-0998.13489 | De Novo, Homology, Library Generation, Annotation, Pipeline, Classification | Present (May 01 2026) | |
| Fastq2LoxDel | https://doi.org/10.1101/2020.07.14.202044 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (May 01 2026) | |
| FiTnEss (Finding Tn-Seq Essentials) | https://doi.org/10.1073/pnas.1900570116 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (May 01 2026) | |
| FindTelomeres | Telomere | Present (May 01 2026) | ||
| FishPi | https://doi.org/10.1186/s13100-025-00342-3 | piRNA | Present (May 01 2026) | |
| FlexDotPlot | https://doi.org/10.1101/2020.04.03.023655 | Visualization, Dot Plot | Present (May 01 2026) | |
| FlexiDot | https://doi.org/10.1093/bioinformatics/bty395 | Visualization, Dot Plot | Present (May 01 2026) | |
| FullSSR | https://doi.org/10.1155/2016/6040124 | Simple Sequence Repeat/Microsatellite, Primer | Present (May 01 2026) | |
| G-IMEx | https://doi.org/10.6026/97320630005221 | Simple Sequence Repeat/Microsatellite, Repeat Extraction, Annotation | Absent (May 01 2026) | |
| GASVPro | https://doi.org/10.1186/gb-2012-13-3-r22 | Structural Variation, NGS/HTS, Paired-End | Absent (May 01 2026) | |
| GC-Profile | https://doi.org/10.2174/1389202915999140328163125 | Genomic Island, GC | Absent (May 01 2026) | |
| GI-Cluster | https://doi.org/10.1142/S0219720018400103 | Genomic Island, GC, Codon Usage, K-mer | Present (May 01 2026) | |
| GI-POP | https://doi.org/10.1016/j.gene.2012.11.063 | Genomic Island, SVM, Annotation | Absent (May 01 2026) | |
| GI-SVM | https://doi.org/10.1142/S0219720016400035 | Genomic Island, SVM, K-mer | Present (May 01 2026) | |
| GIDetector | https://doi.org/10.1186/1471-2164-11-S2-S1 | Genomic Island, Pipeline | Absent (May 01 2026) | |
| GIHunter | https://doi.org/10.4172/jpb.1000322 | Genomic Island, Prediction | Absent (May 01 2026) | |
| GIPSy | https://doi.org/10.1016/j.jbiotec.2015.09.008 | Genomic Island, GC, Homology, HMM | Present (May 01 2026) | |
| GIST | https://doi.org/10.6026/97320630008203 | Genomic Island, Pipeline | Absent (May 01 2026) | |
| GIV | https://doi.org/10.6026/97320630009879 | Genomic Island, Visualization | Absent (May 01 2026) | |
| GMATA | https://doi.org/10.3389/fpls.2016.01350 | Simple Sequence Repeat/Microsatellite, Repeat Extraction, Annotation, Primer | Present (May 01 2026) | |
| GMATo | https://doi.org/10.6026/97320630009541 | Simple Sequence Repeat/Microsatellite, Repeat Annotation | Present (May 01 2026) | |
| GPAC (Genome Presence/Absence Compiler) | https://doi.org/10.1093/molbev/msu276 | Polymorphism, Genotype | Present (May 01 2026) | |
| GRASPER | https://doi.org/10.1089/cmb.2013.0129 | Structural Variation, Repeat, Homology, NGS/HTS, Paired-End | Present (May 01 2026) | |
| GREAM | https://doi.org/10.1371/journal.pone.0133647 | Mammal, Web Server, Genome, Analysis | Present (May 01 2026) | |
| GeIST | https://doi.org/10.1093/bioinformatics/btv350 | Tn-Seq, Transposon Mutagenesis | Present (May 01 2026) | |
| GeneTEFlow | https://doi.org/10.1101/2020.04.28.065862 | RNA-Seq, NGS/HTS, Nextflow | Present (May 01 2026) | |
| Generic Repeat Finder | https://doi.org/10.1104/pp.19.00386 | LTR Retrotransposon, MITE, Inverted Repeat, ITR/TIR/DNA Transposon | Present (May 01 2026) | |
| Genome ARTIST v2 | https://doi.org/10.3390/ijms232012686 | Tn-Seq, Transposon Mutagenesis, Drosophila, ITR/TIR/DNA Transposon | Present (May 01 2026) | |
| GenomeDelta | https://doi.org/10.1186/s13059-024-03459-5 | Polymorphism, Insertion Polymorphism, Short Read | Present (May 01 2026) | |
| GenomeDiff | Dot Plot, Visualization, Virus | Present (May 01 2026) | ||
| GenomeTools | https://doi.ieeecomputersociety.org/10.1109/TCBB.2013.68 | Genome Annotation | Present (May 01 2026) | |
| Gepard | https://doi.org/10.1093/bioinformatics/btm039 | Visualization, Dot Plot | Present (May 01 2026) | |
| GraffiTE | https://doi.org/10.1101/2023.09.11.557209 | Polymorphism, Structural Variation, Long Read, NGS/HTS, Assembly, Pangenome, Graph-Genome, Genotype | Present (May 01 2026) | |
| GraphTyper | https://doi.org/10.1038/ng.3964 | Structural Variation, Short Read, NGS/HTS | Present (May 01 2026) | |
| GraphTyper2 | https://doi.org/10.1038/s41467-019-13341-9 | Structural Variation, Short Read, NGS/HTS | Present (May 01 2026) | |
| Greedier | https://doi.org/10.1093/bioinformatics/btm613 | Homology, Repeat Masking, Nested Insertion, Graph | Present (May 01 2026) | |
| HDRSM (Highly Divergent Repeat Search Method) | https://doi.org/10.1186/s12859-021-03977-0 | SINE | Present (May 01 2026) | |
| HELIANO | https://doi.org/10.1101/2024.02.08.579435 | Helitron, Annotation | Present (May 01 2026) | |
| HERA (Highly Efficient Repeat Assembly) | https://doi.org/10.1038/s41467-019-13355-3 | Long Read, Graph, Assembly | ||
| HIVIntact | https://doi.org/10.1186/s12977-021-00561-5 | Retrovirus, Activity | Present (May 01 2026) | |
| HMMER | https://doi.org/10.1371/journal.pcbi.1000069 | HMM | Present (May 01 2026) | |
| HTdetect | https://doi.org/10.1093/gbe/evu026 | Horizontal Transfer, Homology | Present (May 01 2026) | |
| HashRepeatFinder | https://doi.org/10.1007/s12539-015-0119-6 | De Novo, Library Generation | Absent (May 01 2026) | |
| HelSearch | https://doi.org/10.1073/pnas.0905563106 | Helitron, Structure | Present (May 01 2026) | |
| HelitronFinder | https://doi.org/10.1186/1471-2164-9-51 | Helitron, Structure | Absent (May 01 2026) | |
| HelitronScanner | https://doi.org/10.1073/pnas.1410068111 | Helitron, Structure | Present (May 01 2026) | |
| HiC-TE | https://doi.org/10.1101/2021.12.18.473300 | Hi-C, NGS/HTS, Pipeline | Present (May 01 2026) | |
| HiTE | https://doi.org/10.1101/2023.05.23.541879 | Detection, Annotation | Present (May 01 2026) | |
| HiTea | https://doi.org/10.1101/2020.04.27.060145 | Hi-C, NGS/HTS, Genotype, Polymorphism | Present (May 01 2026) | |
| HomologMiner | https://doi.org/10.1093/bioinformatics/btm048 | Homology, Genome, Comparative | Absent (May 01 2026) | |
| ICEfinder | https://doi.org/10.1093/nar/gky1123 | Link | ICE/Integrative and Conjugative Element, HMM | Absent (May 01 2026) |
| ICEscreen | https://doi.org/10.1093/nargab/lqac079 | ICE/Integrative and Conjugative Element, HMM | Present (May 01 2026) | |
| IDSSR | https://doi.org/10.3390/ijms20143497 | Simple Sequence Repeat/Microsatellite, NGS/HTS, Paired-End, Primer, Repeat Annotation, Polymorphism | Present (May 01 2026) | |
| IGIPT | https://doi.org/10.6026/007/97320630007307 | Genomic Island, Nucleotide Composition, Visualization | Present (May 01 2026) | |
| IMEx | https://doi.org/10.1093/bioinformatics/btm097 | Simple Sequence Repeat/Microsatellite, Annotation, Web Server | Absent (May 01 2026) | |
| INDeGenIUS | https://doi.org/10.1007/s12038-010-0040-4 | Genomic Island, K-mer | ||
| INSurVeyor | https://doi.org/10.1038/s41467-023-38870-2 | Polymorphism, Short Read, NGS/HTS, Paired-End | Present (May 01 2026) | |
| IRF | https://doi.org/10.1101/gr.2542904 | Google drive link | Inverted Repeat, Library Generation | |
| IRescue | https://doi.org/10.1101/2022.09.16.508229 | Single-Cell, NGS/HTS, RNA-Seq, Expression, Transcription | Present (May 01 2026) | |
| IRplus | https://doi.org/10.1093/gbe/evad177 | Link | Inverted Repeat, Plastid, Web Server | Present (May 01 2026) |
| ISAbR_finder | IS Element, AMR/Antibiotic Resistance | Absent (May 01 2026) | ||
| ISCompare | https://doi.org/10.1093/g3journal/jkab181 | IS Element, Genotype, Polymorphism | Present (May 01 2026) | |
| ISEScan | https://doi.org/10.1093/bioinformatics/btx433 | IS Element, HMM, Homology, Library Generation | Present (May 01 2026) | |
| ISMapper | https://doi.org/10.1186/s12864-015-1860-2 | IS Element, Short Read, NGS/HTS, Illumina, Paired-End, Polymorphism, Genotype | Present (May 01 2026) | |
| ISQuest | https://doi.org/10.1093/bioinformatics/btv388 | IS Element, NGS/HTS, Homology | Present (May 01 2026) | |
| IScan | https://doi.org/10.1093/nar/gkm597 | IS Element, Homology | Absent (May 01 2026) | |
| ISsaga | https://doi.org/10.1186/gb-2011-12-3-r30 | Homology, Annotation, IS Element | Absent (May 01 2026) | |
| ISseeker | https://doi.org/10.1099/mgen.0.000062 | IS Element, Homology, Comparative | Present (May 01 2026) | |
| ITIS (Identification of Transposon Insertion Sites) | https://doi.org/10.1186/s12859-015-0507-2 | Genotype, Polymorphism, NGS/HTS | Absent (May 01 2026) | |
| IUPACpal | https://doi.org/10.1186/s12859-021-03983-2 | Inverted Repeat | Present (May 01 2026) | |
| In-seq/Tn-seq | http://doi.org/10.1038/nprot.2011.417 | Tn-Seq, Transposon Mutagenesis | Present (May 01 2026) | |
| InFire | https://doi.org/10.1093/bioinformatics/btr672 | Transposon Mutagenesis, Web Server, Restriction Digestion | Absent (May 01 2026) | |
| InMut-Finder | https://doi.org/10.1186/s12864-021-08206-9 | NGS/HTS, Oxford Nanopore, Tn-Seq, Transposon Mutagenesis | Present (May 01 2026) | |
| Inpactor | https://doi.org/10.3390/biology7020032 | LTR Retrotransposon, Classification, Insertion Time | Present (May 01 2026) | |
| Inpactor2 | https://doi.org/10.1093/bib/bbac511 | LTR Retrotransposon, Classification, Insertion Time, Neural Network | Present (May 01 2026) | |
| InsertionMapper | https://doi.org/10.1186/1471-2164-14-679 | Tn-Seq, Transposon Mutagenesis, NGS/HTS | Present (May 01 2026) | |
| IntegronFinder | https://doi.org/10.1093/nar/gkw319 | Link | Integron, HMM | Present (May 01 2026) |
| IntegronFinder 2.0 | https://doi.org/10.3390/microorganisms10040700 | Integron, HMM | Present (May 01 2026) | |
| Invade | https://doi.org/10.1093/molbev/msz079 | Simulation, piRNA, Genome | Present (May 01 2026) | |
| IpiRId | https://doi.org/10.1371/journal.pone.0179787 | piRNA, SVM | Absent (May 01 2026) | |
| IslandCafe | https://doi.org/10.1534/g3.119.400562 | Genomic Island | Present (May 01 2026) | |
| IslandPath-DIMOB | https://doi.org/10.1093/bioinformatics/bty095 | Genomic Island, HMM, Homology, K-mer | Present (May 01 2026) | |
| IslandPick | https://doi.org/10.1186/1471-2105-9-329 | Genomic Island, Homology, Comparative | Absent (May 01 2026) | |
| IslandViewer 4 | https://doi.org/10.1093/bioinformatics/btp030 | Genomic Island, Visualization, Web Server | Absent (May 01 2026) | |
| JDotter | https://doi.org/10.1093/bioinformatics/btg406 | Dot Plot, Visualization | Present (May 01 2026) | |
| Jitterbug | https://doi.org/10.1186/s12864-015-1975-5 | Paired-End, NGS/HTS, Polymorphism, Genotype, | Present (May 01 2026) | |
| KKSC Significance Test | https://doi.org/10.1371/journal.pcbi.1004812 | Polymorphism, Genotype, LINE/Non-LTR Retrotransposon, Age, Speciation | Present (May 01 2026) | |
| L1EM | https://doi.org/10.1093/bioinformatics/btz724 | Expression, Transcription, LINE1, LINE/Non-LTR Retrotransposon, Activity, NGS/HTS | Present (May 01 2026) | |
| L1PD (LINE-1 Pattern Detection) | https://doi.org/10.1186/s12859-022-04907-4 | LINE1, LINE/Non-LTR Retrotransposon, K-mer | Present (May 01 2026) | |
| L1Seq | https://doi.org/10.1101/gr.106419.110 | LINE/Non-LTR Retrotransposon, LINE1 | Present (May 01 2026) | |
| LAST | https://doi.org/10.1186/s13059-015-0670-9 | Alignment, Repeat | Absent (May 01 2026) | |
| LIONS | https://doi.org/10.1093/bioinformatics/btz130 | RNA-Seq, Transcription | Present (May 01 2026) | |
| LTR Annotator | https://doi.org/10.17706/ijbbb.2015.5.3.165-174 | LTR Retrotransposon, Library Generation, Annotation | ||
| LTR_FINDER | https://doi.org/10.1093/nar/gkm286 | LTR Retrotransposon, Structure, Web Server | Absent (May 01 2026) | |
| LTR_FINDER_parallel | https://doi.org/10.1186/s13100-019-0193-0 | LTR Retrotransposon, Structure, HPC | Present (May 01 2026) | |
| LTR_MINER | https://doi.org/10.1186/gb-2004-5-10-r79 | LTR Retrotransposon, Solo-LTR, Filtering, Nested Insertion | ||
| LTR_STRUC | https://doi.org/10.1093/bioinformatics/btf878 | LTR Retrotransposon, Structure | Present (May 01 2026) | |
| 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 (May 01 2026) | |
| LTRclassifier | https://doi.org/10.1080/2159256X.2016.1241050 | Link | LTR Retrotransposon, HMM, Classification, Web Server | Present (May 01 2026) |
| LTRdigest | https://doi.org/10.1093/nar/gkp759 | LTR Retrotransposon, Web Server, Structure, Classification | Present (May 01 2026) | |
| LTRharvest | https://doi.org/10.1186/1471-2105-9-18 | Link | LTR Retrotransposon, Structure | Present (May 01 2026) |
| LTRphyler | https://doi.org/10.1186/1471-2229-13-172 | LTR Retrotransposon, Classification | Absent (May 01 2026) | |
| LTRpred | https://doi.org/10.21105/joss.02170 | De Novo, Homology, LTR Retrotransposon, Annotation | Absent (May 01 2026) | |
| LTRsift | https://doi.org/10.1186/1759-8753-3-18 | Link | De Novo, LTR Retrotransposon, Visualization, Library Generation, Annotation | Absent (May 01 2026) |
| LTRtype | https://doi.org/10.3389/fpls.2017.00402 | LTR Retrotransposon, Nested Insertion, Homology, | Absent (May 01 2026) | |
| LoRTE | https://doi.org/10.1186/s13100-017-0088-x | Long Read, PacBio, NGS/HTS, Genotype, Polymorphism, Indel, Homology | Absent (May 01 2026) | |
| LoRTIS-SS | https://doi.org/10.1101/2022.05.26.493556 | Long Read, NGS/HTS, Oxford Nanopore, Tn-Seq, Transposon Mutagenesis | Present (May 01 2026) | |
| LocaTR | https://doi.org/10.1186/s12864-016-3043-1 | LTR Retrotransposon, Homology, Structure, Annotation | Present (May 01 2026) | |
| LocusMasterTE | https://doi.org/10.1101/2023.03.21.533716 | NGS/HTS, Long Read, Expression, Transcription, RNA-Seq | Present (May 01 2026) | |
| LongRepMarker | https://doi.org/10.1093/nar/gkab563 | De Novo, K-mer, Library Generation, Long Read, Short Read | Present (May 01 2026) | |
| Look4LTRs | https://doi.org/10.1186/s13100-024-00317-w | LTR Retrotransposon, Nested Insertion, Annotation | Present (May 01 2026) | |
| LtrDetector | https://doi.org/10.1186/s12864-019-5796-9 | De Novo, LTR Retrotransposon, Structure, Annotation, Visualization | Present (May 01 2026) | |
| Lumpy | https://doi.org/10.1186/gb-2014-15-6-r84 | Structural Variation | Present (May 01 2026) | |
| MAGenTA | https://doi.org/10.1093/bioinformatics/btx320 | Web Server, Tn-Seq, Transposon Mutagenesis, NGS/HTS, Visualization, Analysis | Present (May 01 2026) | |
| MAK (MITE Analysis Kit) | https://doi.org/10.1093/nar/gkg531 | MITE, Homology, Annotation, ITR/TIR/DNA Transposon | Absent (May 01 2026) | |
| MANTIS | http://doi.org/10.18632/oncotarget.13918 | Simple Sequence Repeat/Microsatellite, Instability, Cancer, NGS/HTS | Present (May 01 2026) | |
| MASiVE | https://doi.org/10.1093/bioinformatics/btq454 | LTR Retrotransposon, Sirevirus, Structure, Repeat Extraction | Absent (May 01 2026) | |
| MATES (Multi-mapping Alignment for TE loci quantification in Single-cell) | https://doi.org/10.1038/s41467-024-53114-7 | Single-Cell, Insertion Polymorphism, Polymorphism | Present (May 01 2026) | |
| MCHelper | https://doi.org/10.1101/2023.10.17.562682 | Automated Curation, Classification | Present (May 01 2026) | |
| ME-Scan | https://doi.org/10.1186/s13100-020-00207-x | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (May 01 2026) | |
| MEGAnE | https://doi.org/10.1101/2022.03.25.485726 | Github | Genotype, Polymorphism, NGS/HTS, Short Read | Present (May 01 2026) |
| MELT | https://doi.org/10.1101/gr.218032.116 | Genotype, Polymorphism, Illumina, Paired-End, NGS/HTS | Present (May 01 2026) | |
| MGERT | https://doi.org/10.1186/s13100-019-0163-6 | Conserved Domain, Repeat Extraction, De Novo, Library Generation, Repeat Extraction | Present (May 01 2026) | |
| MGEScan | https://doi.org/10.1093/bioinformatics/btw157 | Web Server, LTR Retrotransposon, LINE/Non-LTR Retrotransposon, HMM | Present (May 01 2026) | |
| MGEfinder | https://doi.org/10.1016/j.chom.2019.10.022 | Archaea, Bacteria, , NGS/HTS, Polymorphism, Library Generation | Present (May 01 2026) | |
| MIRU-VNTRplus | https://doi.org/10.1093/nar/gkq351 | Tuberculosis, Genotype, Tandem Repeat, Web Server | Absent (May 01 2026) | |
| MIRU-profiler | https://doi.org/10.7717/peerj.5090 | Tuberculosis, Genotype, Tandem Repeat | Present (May 01 2026) | |
| 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 (May 01 2026) | |
| MITE Digger | https://doi.org/10.1186/1471-2105-14-186 | MITE, Homology, Annotation, ITR/TIR/DNA Transposon | Present (May 01 2026) | |
| MITE Tracker | https://doi.org/10.1186/s12859-018-2376-y | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Present (May 01 2026) | |
| MITE-Hunter | https://doi.org/10.1093/nar/gkq862 | MITE, Structure, Annotation, ITR/TIR/DNA Transposon | Absent (May 01 2026) | |
| MJSD | https://doi.org/10.1093/nar/gkp576 | Genomic Island, Nucleotide Composition | ||
| MOBSTER | https://doi.org/10.1186/s13059-014-0488-x | NGS/HTS, Genotype, Polymorphism, | Present (May 01 2026) | |
| MSGIP | https://doi.org/10.1371/journal.pone.0146352 | Genomic Island, Mean Shift Algorithm | Present (May 01 2026) | |
| MSIsensor | https://doi.org/10.1093/bioinformatics/btt755 | Simple Sequence Repeat/Microsatellite, Instability, Polymorphism, Genotype, NGS/HTS, Cancer | Present (May 01 2026) | |
| MTGIpick | https://doi.org/10.1093/bib/bbw118 | Genomic Island, K-mer | Present (May 01 2026) | |
| 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 (May 01 2026) | |
| MacSyFinder | https://doi.org/10.1371/journal.pone.0110726 | CRISPR, HMM | Present (May 01 2026) | |
| McClintock | https://doi.org/10.1534/g3.117.043893 | Genotype, Polymorphism, NGS/HTS | Present (May 01 2026) | |
| McClintock2 | https://doi.org/10.1101/2023.02.13.528343 | Genotype, Polymorphism, NGS/HTS | Present (May 01 2026) | |
| MegaLTR | https://doi.org/10.3389/fpls.2023.1237426 | Webserver | LTR Retrotransposon, Detection, Annotation, Web Server, Pipeline | Present (May 01 2026) |
| MetaCompare | https://doi.org/10.1093/femsec/fiy079 | NGS/HTS, Metagenomics, AMR/Antibiotic Resistance, BLAST, Pathogen | Present (May 01 2026) | |
| MetaPhage | https://doi.org/10.1101/2022.04.17.488583 | NGS/HTS, Metagenomics, Annotation, Classification, Prophage/Bacteriophage | Present (May 01 2026) | |
| MiMSI | https://doi.org/10.1101/2020.09.16.299925 | Simple Sequence Repeat/Microsatellite, Cancer | Present (May 01 2026) | |
| MindTheGap | https://doi.org/10.1093/bioinformatics/btu545 | NGS/HTS, Polymorphism, Genotype, K-mer | Present (May 01 2026) | |
| MiteFinder | https://doi.org/10.1109/BIBM.2017.8217644 | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Present (May 01 2026) | |
| MiteFinderII | https://doi.org/10.1186/s12920-018-0418-y | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Present (May 01 2026) | |
| MobileElementFinder | https://doi.org/10.1093/jac/dkaa390 | IS Element, AMR/Antibiotic Resistance, Plasmid, Homology, Web Server | Absent (May 01 2026) | |
| MobilomeFINDER | https://doi.org/10.1093/nar/gkm380 | Genomic Island, Microarray, Web Server | Absent (May 01 2026) | |
| ModuleOrganizer | https://doi.org/10.1186/1471-2105-11-474 | Sequence Motif, Visualization, Web Server | ||
| MyDGR | https://doi.org/10.1093/nar/gkz329 | DGR/Diversity Generating Retroelement, Annotation, BLAST, Alignment, Web Server | Present (May 01 2026) | |
| NCRF | https://doi.org/10.1093/bioinformatics/btz484 | Long Read, NGS/HTS, Tandem Repeat, De Novo | Present (May 01 2026) | |
| NGSEP | https://doi.org/10.1002/aps3.11520 | https://sourceforge.net/projects/ngsep/ | Repeat Masking, Annotation | Present (May 01 2026) |
| NGSEP (Next-Generation Sequencing Experience Platform) | https://doi.org/10.1002/aps3.11520 | Github | NGS/HTS, Homology, Long Read, Annotation | Present (May 01 2026) |
| NTRFinder | https://doi.org/10.1093/nar/gkr1070 | Tandem Repeat | ||
| NanoCasTE | https://doi.org/10.1111/jipb.13555 | NGS/HTS, Oxford Nanopore, Cas9, Polymorphism, Genotype | Present (May 01 2026) | |
| NanoSatellite | https://doi.org/10.1186/s13059-019-1856-3 | NGS/HTS, Oxford Nanopore, Tandem Repeat | Present (May 01 2026) | |
| NanoTRF | https://doi.org/10.3390/plants11162103 | NGS/HTS, Oxford Nanopore, Tandem Repeat | Present (May 01 2026) | |
| NanoVar | https://doi.org/10.1186/s13059-020-01968-7 | NGS/HTS, Oxford Nanopore, Polymorphism, Genotype | Present (May 01 2026) | |
| NanoWgsTE | https://doi.org/10.1101/2021.06.11.448052 | Oxford Nanopore, CRISPR, Eukaryotic Transposon | Present (May 01 2026) | |
| NearTrans | https://doi.org/10.1007/978-3-319-78723-7_32 | Expression, Transcription, Analysis, Pipeline | ||
| NeuralTE | https://doi.org/10.1101/2024.01.21.576519 | TE Classification, Eukaryotic Retrotransposon, Eukaryotic Transposon | Present (May 01 2026) | |
| OASIS | https://doi.org/10.1101/2020.11.02.365809 | IS Element, Homology, Classification | Present (May 01 2026) | |
| OMWSA (Optimized Moving Window Spectral Analysis) | https://doi.org/10.1093/bioinformatics/btm008 | Visualization, Repeat | Absent (May 01 2026) | |
| OSTRFPD | https://doi.org/10.1177%2F1176934319843130 | Simple Sequence Repeat/Microsatellite, Alignment, Repeat Extraction, Annotation | Present (May 01 2026) | |
| One_code_to_find_them_all | https://doi.org/10.1186/1759-8753-5-13 | Repeat Extraction, Abundance | Present (May 01 2026) | |
| P-Clouds | https://doi.org/10.1016/j.ab.2008.05.015 | De Novo, Library Generation | ||
| PADLOC (Prokaryotic Antiviral Defence LOCator) | https://doi.org/10.1093/nar/gkac400 | Web Server, Antiviral, Virus | Present (May 01 2026) | |
| PAI-IDA | https://doi.org/10.1016/S0378-1097(03)00204-0 | Genomic Island, GC, Codon Usage | ||
| PASTEC | https://doi.org/10.1371/journal.pone.0091929 | Link | Classification | Present (May 01 2026) |
| PATIMDB | https://doi.org/10.1002/0471142727.mb1907s86 | Tn-Seq, Transposon Mutagenesis | Absent (May 01 2026) | |
| PAtChER | https://doi.org/10.1101/2021.08.25.457666 | ChIP-Seq | Present (May 01 2026) | |
| PHACTS | https://doi.org/10.1093/bioinformatics/bts014 | Prophage/Bacteriophage, Classification | Present (May 01 2026) | |
| PHAST | https://doi.org/10.1093/nar/gkr485 | Prophage/Bacteriophage, Web Server, Homology, Annotation, Visualization | Absent (May 01 2026) | |
| PHASTER | https://doi.org/10.1093/nar/gkw387 | Prophage/Bacteriophage, Web Server, Homology, Annotation, Visualization | Absent (May 01 2026) | |
| PIATEA | HMM, Annotation Track | Present (May 01 2026) | ||
| PILER | https://doi.org/10.1093/bioinformatics/bti1003 | De Novo, Library Generation | Present (May 01 2026) | |
| PILFER | https://doi.org/10.1016/j.ygeno.2017.12.005 | piRNA, RNA-Seq, NGS/HTS | Present (May 01 2026) | |
| PIMMS (Pragmatic Insertional Mutation Mapping System) | https://doi.org/10.3389/fgene.2015.00139 | NGS/HTS, Tn-Seq | Present (May 01 2026) | |
| PIMMS-Dash | https://doi.org/10.1016/j.csbj.2024.10.025 | Link | Web Server, Transposon Mutagenesis, Tn-Seq | Present (May 01 2026) |
| PIPS | https://doi.org/10.1371/journal.pone.0030848 | Genomic Island, Pathogenicity Island, Prediction | Absent (May 01 2026) | |
| PPR-Meta | https://doi.org/10.1093/gigascience/giz066 | Link | Prophage/Bacteriophage, Plasmid, Deep Learning | Absent (May 01 2026) |
| PRAP | https://doi.org/10.1093/bioinformatics/btt482 | De Novo, Library Generation, Repeat Masking, Archaea, Bacteria | Present (May 01 2026) | |
| PSSV | https://doi.org/10.1093/bioinformatics/btw605 | Structural Variation, NGS/HTS | Absent (May 01 2026) | |
| PTEMD | https://doi.org/10.1093/dnares/dsw011 | Short Read, NGS/HTS, Genotype, Polymorphism, De Novo | Absent (May 01 2026) | |
| PacmonSTR | https://doi.org/10.1093/bioinformatics/btu437 | Tandem Repeat, NGS/HTS, Long Read, HMM, Homology | Present (May 01 2026) | |
| PaliDIS | https://doi.org/10.1099/mgen.0.000917 | IS Element, Metagenomics, Annotation | Present (May 01 2026) | |
| [Pannagram (Pan-genome alignment, Annotation, Analysis and Diagrams)] | https://doi.org/10.1101/2025.02.07.637071 | Insertion Polymorphism, Polymorphism, Pangenome, Structural Variation | ||
| Paragraph | https://doi.org/10.1186/s13059-019-1909-7 | Graph, Structural Variation, Genotype, NGS/HTS, Short Read | Present (May 01 2026) | |
| ParasiTE | https://doi.org/10.1101/2022.09.21.507229 | Long Read, NGS/HTS, RNA-Seq, Expression, Transcription | Present (May 01 2026) | |
| PeSV-Fisher | https://doi.org/10.1371/journal.pone.0063377 | Structural Variation | ||
| PerSVade | https://doi.org/10.1101/2021.11.23.469703 | Structural Variation, Pipeline | Present (May 01 2026) | |
| PhaGenus | https://doi.org/10.1093/bib/bbad408 | Prophage/Bacteriophage, Classification | Present (May 01 2026) | |
| Phage Commander | https://doi.org/10.1101/2020.11.11.378802 | Prophage/Bacteriophage, Pipeline | Present (May 01 2026) | |
| PhageAI | https://doi.org/10.1101/2020.07.11.198606 | Prophage/Bacteriophage, Web Server, Machine Learning, Classification | Present (May 01 2026) | |
| PhageWeb | https://doi.org/10.3389/fgene.2018.00644 | Prophage/Bacteriophage, Web Server, GC, tRNA | Absent (May 01 2026) | |
| Phage_Finder | https://doi.org/10.1093/nar/gkl732 | Prophage/Bacteriophage, Homology, HMM | Present (May 01 2026) | |
| PhiSpy | https://doi.org/10.1093/nar/gks406 | Prophage/Bacteriophage, Homology | Present (May 01 2026) | |
| Phigaro | https://doi.org/10.1093/bioinformatics/btaa250 | Prophage/Bacteriophage, Annotation | Present (May 01 2026) | |
| Phobos | Simple Sequence Repeat/Microsatellite, Library Generation | Present (May 01 2026) | ||
| PhyLTR | LTR Retrotransposon, Annotation, Pipeline, Gene Conversion, Classification, Phylogeny | Present (May 01 2026) | ||
| PiRATE | https://doi.org/10.1186/s12864-018-4763-1 | Web Server, Homology, HMM, Structure, De Novo, Classification, Library Generation, Annotation | Present (May 01 2026) | |
| Piano | https://doi.org/10.1186/s12859-014-0419-6 | piRNA, SVM, Classification, Web Server | Absent (May 01 2026) | |
| Pibomd | https://doi.org/10.1039/c4mb00447g | piRNA, SVM | ||
| Pindel | https://doi.org/10.1093/bioinformatics/btp394 | Short Read, Paired-End, Structural Variation, NGS/HTS | Present (May 01 2026) | |
| PingPongPro | https://doi.org/10.1093/bioinformatics/bty578 | piRNA, RNA-Seq, NGS/HTS | Present (May 01 2026) | |
| PlasForest | https://doi.org/10.1186/s12859-021-04270-w | Plasmid, Homology, Classification | Present (May 01 2026) | |
| PlasLR | https://doi.org/10.1101/2021.06.14.448306 | Plasmid, Long Read | Present (May 01 2026) | |
| PlasTrans | https://doi.org/10.1099/mgen.0.000459 | Plasmid | Present (May 01 2026) | |
| Plasflow | https://doi.org/10.1093/nar/gkx1321 | Plasmid, Metagenomics, Neural Network | Present (May 01 2026) | |
| PlasmidFinder | https://doi.org/10.1128/aac.02412-14 | Plasmid, Homology | Absent (May 01 2026) | |
| PlasmidHunter | https://doi.org/10.1101/2023.02.01.526640 | Link | Plasmid, Web Server | Present (May 01 2026) |
| PlasmidTron | https://doi.org/10.1099/mgen.0.000164 | Plasmid, K-mer | Present (May 01 2026) | |
| PlotRep | https://doi.org/10.1093/nar/gkl263 | Dot Plot, Visualization, Repeat Merging | Absent (May 01 2026) | |
| PoPoolationTE | https://doi.org/10.1093/molbev/msw137 | Genotype, Polymorphism, NGS/HTS | Present (May 01 2026) | |
| PolyMorphPredict | https://doi.org/10.3389/fpls.2018.01966 | Simple Sequence Repeat/Microsatellite, Primer, Web Server | Absent (May 01 2026) | |
| PostSV | https://doi.org/10.1177/1177932219892957 | Structural Variation, NGS/HTS, SVM | ||
| PredictBias | https://content.iospress.com/articles/in-silico-biology/isb00352 | Genomic Island, Web Server, Homology | Present (May 01 2026) | |
| PrinTE | Forward simulator of transposable-element genome evolution | Present (June 05 2026) | ||
| ProGeRF | http://doi.org/10.1155/2015/394157 | Simple Sequence Repeat/Microsatellite, Annotation | Absent (May 01 2026) | |
| Process_hits | https://doi.org/10.1186/1756-0500-4-482 | Repeat Extraction, Alignment | Present (May 01 2026) | |
| ProphET | https://doi.org/10.1371/journal.pone.0223364 | Prophage/Bacteriophage, Homology, Annotation | Present (May 01 2026) | |
| Prophage Finder | https://content.iospress.com/articles/in-silico-biology/isb00235 | Prophage/Bacteriophage, Homology | ||
| Prophinder | https://doi.org/10.1093/bioinformatics/btn043 | Prophage/Bacteriophage, Homology | Absent (May 01 2026) | |
| Pysim-sv | https://doi.org/10.1186/s12859-017-1464-8 | Structural Variation, NGS/HTS, Simulation | Present (May 01 2026) | |
| QDD | https://doi.org/10.1093/bioinformatics/btp670 | Simple Sequence Repeat/Microsatellite, Primer | Absent (May 01 2026) | |
| RAIDER | https://doi.org/10.1007/978-3-319-02624-4_16 | De Novo, Repeat, Library Generation | ||
| 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 (May 01 2026) | |
| RAREFAN (RAyt/REpin Finder and ANalyzer) | https://doi.org/10.24072/pcjournal.244 | Web Server, REPIN/RAYT, Annotation | Present (May 01 2026) | |
| RBR | https://doi.org/10.1093/bioinformatics/btl368 | Expression, Transcription, RNA-Seq, Repeat Masking, De Novo | Absent (May 01 2026) | |
| REPCLASS | https://uta-ir.tdl.org/uta-ir/handle/10106/455 | Classification | Present (May 01 2026) | |
| REPET | https://doi.org/10.1371/journal.pone.0016526 | Link | De Novo, Homology, Structure, Library Generation, Annotation | Present (May 01 2026) |
| REPdenovo | https://doi.org/10.1371/journal.pone.0150719 | Short Read, NGS/HTS, De Novo, Assembly | Present (May 01 2026) | |
| REPuter | https://doi.org/10.1093/nar/29.22.4633 | Repeat, Library Generation, De Novo | Absent (May 01 2026) | |
| 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 (May 01 2026) |
| REannotate | https://doi.org/10.1186/1471-2164-9-614 | Annotation Parsing, Nested Insertion | Present (May 01 2026) | |
| REdiscoverTE | https://doi.org/10.1038/s41467-019-13035-2 | Expression, Transcription, RNA-Seq | Present (May 01 2026) | |
| RFPlasmid | https://doi.org/10.1101/2020.07.31.230631 | Link | Plasmid, Resistance, AMR/Antibiotic Resistance, K-mer, Homology | Present (May 01 2026) |
| RIPCAL | https://doi.org/10.1186/1471-2105-9-478 | RIP/Repeat-Induced Point Mutation, Mutation, Alignment, Repeat | Present (May 01 2026) | |
| RISCI (Repeat Induced Sequence Changes Identifier) | https://doi.org/10.1186/1471-2105-11-609 | NGS/HTS, Genotype, Polymorphism | Absent (May 01 2026) | |
| RJPrimers | https://doi.org/10.1093/nar/gkq425 | Homology, Primer | Absent (May 01 2026) | |
| RNA2DSearch | https://doi.org/10.1261/rna.1264109 | RNA Localization, Prediction, Web Server | Absent (May 01 2026) | |
| RPT (Repeat Pattern Toolkit) | Repeat Annotation | |||
| RSPB | https://doi.org/10.1093/molbev/msr282 | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Absent (May 01 2026) | |
| RSVSim | https://doi.org/10.1093/bioinformatics/btt198 | Structural Variation, Simulation | Present (May 01 2026) | |
| RTAnalyzer | https://doi.org/10.1093/nar/gkm313 | LINE1, LINE/Non-LTR Retrotransposon, Homology | Absent (May 01 2026) | |
| RTclass1 | https://doi.org/10.1016/j.gene.2009.07.019 | Classification, LINE/Non-LTR Retrotransposon | Present (May 01 2026) | |
| ReAS | https://doi.org/10.1371/journal.pcbi.0010043 | Email for files: ReAS@genomics.org.cn | De Novo, Library Generation, NGS/HTS | |
| ReAlignerV | https://doi.org/10.1186/1471-2105-9-112 | Alignment | ||
| ReDoSt | https://doi.org/10.1186/1471-2164-12-621 | DIRS, Eukaryotic Retrotransposon, Homology, Structure, Annotation | Absent (May 01 2026) | |
| Red | https://doi.org/10.1186/s12859-015-0654-5 | Machine Learning, De Novo, Library Generation | ||
| RelocaTE2 | https://doi.org/10.7717/peerj.2942 | Polymorphism, Genotype, NGS/HTS | Present (May 01 2026) | |
| RepAHR | https://doi.org/10.1186/s12859-020-03779-w | De Novo, Library Generation, NGS/HTS, K-mer | Present (May 01 2026) | |
| RepARK | https://doi.org/10.1093/nar/gku210 | De Novo, Library Generation, NGS/HTS | Present (May 01 2026) | |
| RepBox | https://doi.org/10.1186/s12859-023-05419-5 | TE Detection, TE Annotation, Plants | Present (May 01 2026) | |
| RepBox | https://doi.org/10.1186/s12859-023-05419-5 | Detection, Annotation, Classification, Pipeline | Present (May 01 2026) | |
| RepEnrich | https://doi.org/10.1186/1471-2164-15-583 | NGS/HTS, RNA-Seq, Expression | Present (May 01 2026) | |
| RepEnrich2 | NGS/HTS, RNA-Seq, Expression | Present (May 01 2026) | ||
| RepExpress | https://doi.org/10.1002/cpz1.206 | Pipeline, RNA-Seq, Expression | Present (May 01 2026) | |
| RepLoc | https://doi.org/10.1093/bib/bbaa086 | Repeat, K-mer, Visualization, Annotation, Web Server | Present (May 01 2026) | |
| RepLong | https://doi.org/10.1093/bioinformatics/btx717 | De Novo, Long Read, NGS/HTS | Present (May 01 2026) | |
| RepMiner | https://doi.org/10.1101/gr.083360.108 | Repeat, Library Generation, De Novo | Present (May 01 2026) | |
| RepSeeker | https://ieeexplore.ieee.org/document/5260704 | Repeat, Library Generation, De Novo | ||
| Repeat Enrichment Estimator | https://doi.org/10.1186/gb-2010-11-6-r69 | NGS/HTS, ChIP-Seq, Repeat, Web Server | Absent (May 01 2026) | |
| Repeat Expansion Viewer (REViewer) | Short Read, NGS/HTS, Short Tandem Repeat | Present (May 01 2026) | ||
| RepeatAnalyzer | https://doi.org/10.1186/s12864-016-2686-2 | Simple Sequence Repeat/Microsatellite, Summary, Genotype | Present (May 01 2026) | |
| RepeatCraft | https://doi.org/10.1093/bioinformatics/bty745 | Nested Insertion, Visualization | Present (May 01 2026) | |
| RepeatExplorer | https://doi.org/10.1093/bioinformatics/btt054 | Link | De Novo, Library Generation, Annotation, NGS/HTS | Present (May 01 2026) |
| RepeatFiller | https://doi.org/10.1093/gigascience/giz132 | Genome Alignment, Repeat | Present (May 01 2026) | |
| RepeatFinder | https://doi.org/10.1186/gb-2001-2-8-research0027 | Library Generation | Present (May 01 2026) | |
| RepeatGluer | https://doi.org/10.1101/gr.2395204 | Repeat Annotation | ||
| RepeatMasker | Repeat Masking, Annotation | Present (May 01 2026) | ||
| RepeatModeler | https://doi.org/10.1073/pnas.1921046117 | GitHub | De Novo, Library Generation, Structure, Seed Alignment, Classification | Absent (May 01 2026) |
| RepeatProfiler | https://doi.org/10.1101/2020.05.22.111252 | NGS/HTS, Short Read, Visualization, Repeat | Present (May 01 2026) | |
| RepeatRunner | https://doi.org/10.1016/j.gene.2006.09.011 | De Novo, Library Generation | Present (May 01 2026) | |
| RepeatScout | https://doi.org/10.1093/bioinformatics/bti1018 | De Novo, Library Generation | Present (May 01 2026) | |
| RepeatSeq | https://doi.org/10.1093/nar/gks981 | Simple Sequence Repeat/Microsatellite, Genotype, Polymorphism, NGS/HTS | Present (May 01 2026) | |
| Repguide | CRISPR, gRNA, Repeat | Present (May 01 2026) | ||
| Repsc | Expression, RNA-Seq, Single-Cell | Present (May 01 2026) | ||
| Repseek | https://doi.org/10.1093/bioinformatics/btl519 | Repeat, Library Generation, De Novo | Absent (May 01 2026) | |
| RetroMap | https://doi.org/10.1186/gb-2004-5-10-r78 | LTR Retrotransposon, Visualization | Absent (May 01 2026) | |
| RetroSnake | https://doi.org/10.1101/2022.04.08.487607 | NGS/HTS, ERV/Endogenous Retrovirus, Annotation | Present (May 01 2026) | |
| RetroSom | https://doi.org/10.1101/660779 | Machine Learning, NGS/HTS, Genotype, Polymorphism | Present (May 01 2026) | |
| RetroTector | https://doi.org/10.1093/nar/gkm515 | ERV/Endogenous Retrovirus | Present (May 01 2026) | |
| Retroseq | https://doi.org/10.1093/bioinformatics/bts697 | Genotype, Polymorphism, NGS/HTS, Illumina, Paired-End | Present (May 01 2026) | |
| SAT | https://doi.org/10.1186/1471-2105-8-465 | Simple Sequence Repeat/Microsatellite, Primer, Library Generation, Web Server | Absent (May 01 2026) | |
| SATEComp | Link | Homology, Keyword Search, Web Server | Absent (May 01 2026) | |
| SCNVSim | https://doi.org/10.1186/s12859-015-0502-7 | CNV/Copy Number Variation, Simulation, Structural Variation | Present (May 01 2026) | |
| SCRAMble | https://doi.org/10.1038/s41436-020-0749-x | NGS/HTS, Genotype, Polymorphism, Paired-End | Present (May 01 2026) | |
| SECNVs | https://doi.org/10.3389/fgene.2020.00082 | CNV/Copy Number Variation, Simulation, Expression | Present (May 01 2026) | |
| SERpredict | https://doi.org/10.1186/1471-2156-8-78 | RNA-Seq, Expression, Homology | ||
| SID (Specific Insertions Detector) | https://doi.org/10.1093/gigascience/gix066 | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (May 01 2026) | |
| SIGAR | https://doi.org/10.1101/2020.05.05.079426 | NGS/HTS, Short Read, Split Read | Present (May 01 2026) | |
| SIGI-HMM | https://doi.org/10.1186/1471-2105-7-142 | Genomic Island, Codon Usage, HMM | Absent (May 01 2026) | |
| SINE-Finder | https://doi.org/10.1105/tpc.111.088682 | SINE, Homology, Motif, Library Generation | Absent (May 01 2026) | |
| SINE_Scan | https://doi.org/10.1093/bioinformatics/btw718 | SINE, Library Generation, Annotation | Present (May 01 2026) | |
| SINEsFIND | https://doi.org/10.1093/dnares/dsw048 | SINE, Expression, RNA-Seq, NGS/HTS | Present (May 01 2026) | |
| SMaRTFinder | Repeat, Annotation | Absent (May 01 2026) | ||
| SPLITREADER | https://doi.org/10.7554/eLife.15716.001 | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (May 01 2026) | |
| SQUID | https://doi.org/10.1186/s13059-018-1421-5 | RNA-Seq, Expression, NGS/HTS, Structural Variation, Fusion | Present (May 01 2026) | |
| SQuIRE | https://doi.org/10.1093/nar/gky1301 | NGS/HTS, RNA-Seq, Expression | Present (May 01 2026) | |
| SRC (Spark-based RepeatClassifier) | https://doi.org/10.1101/2021.06.03.446998 | RepeatMasker, Classification | Present (May 01 2026) | |
| SRF | https://doi.org/10.1093/bioinformatics/bth103 | Repeat, Web Server | Absent (May 01 2026) | |
| SRF (Satellite Repeat Finder) | https://doi.org/10.1101/gr.278005.123 | Simple Sequence Repeat/Microsatellite, NGS/HTS, Library Generation | Present (May 01 2026) | |
| SSR Locator | http://dx.doi.org/10.1155/2008/412696 | Simple Sequence Repeat/Microsatellite, Primer, PCR, Library Generation | Absent (May 01 2026) | |
| SSR Primer | https://doi.org/10.1093/bioinformatics/bth104 | Simple Sequence Repeat/Microsatellite, Primer, Library Generation | Absent (May 01 2026) | |
| SSRIT | Simple Sequence Repeat/Microsatellite, Summary | Present (May 01 2026) | ||
| SSRfinder | https://doi.org/10.1023/A:1026346121217 | Simple Sequence Repeat/Microsatellite, EST, Expression | ||
| STAR | https://doi.org/10.1093/bioinformatics/bth335 | Tandem Repeat, Annotation | Present (May 01 2026) | |
| STEAK | https://doi.org/10.1093/ve/vex023 | NGS/HTS, Genotype, Polymorphism, Annotation | Present (May 01 2026) | |
| STRipy | https://doi.org/10.1101/2021.06.13.448220 | Link | Short Tandem Repeat, Genotype, NGS/HTS | Present (May 01 2026) |
| STRling | https://doi.org/10.1186/s13059-022-02826-4 | Short Tandem Repeat, Annotation, NGS/HTS | Present (May 01 2026) | |
| SURVIVOR | https://doi.org/10.1038/ncomms14061 | Structural Variation, NGS/HTS, Simulation | Present (May 01 2026) | |
| 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 (May 01 2026) | |
| SV2 | https://doi.org/10.1093/bioinformatics/btx813 | Structural Variation, Machine Learning, Paired-End | Present (May 01 2026) | |
| SVDSS | https://doi.org/10.1038/s41592-022-01674-1 | NGS/HTS, Structural Variation, Long Read | Present (May 01 2026) | |
| SVDetect | https://doi.org/10.1093/bioinformatics/btq293 | NGS/HTS, Structural Variation, Paired-End | Present (May 01 2026) | |
| SVEngine | https://doi.org/10.1093/gigascience/giy081 | Structural Variation, Simulation | Present (May 01 2026) | |
| SVIM | https://doi.org/10.1093/bioinformatics/btz041 | NGS/HTS, Long Read, Structural Variation | Present (May 01 2026) | |
| SVM2 | https://doi.org/10.1093/nar/gks606 | Structural Variation, Supervised Learning | ||
| SVPV | https://doi.org/10.1093/bioinformatics/btx117 | Structural Variation, Visualization | Present (May 01 2026) | |
| SVXplorer | https://doi.org/10.1371/journal.pcbi.1007737 | NGS/HTS, Paired-End, Structural Variation | Present (May 01 2026) | |
| SVelter | https://doi.org/10.1186/s13059-016-0993-1 | Structural Variation, NGS/HTS | Present (May 01 2026) | |
| SVmine | https://doi.org/10.1093/bioinformatics/btx455 | Structural Variation, Pipeline | Present (May 01 2026) | |
| SWGIS v2.0 | https://doi.org/10.1186/s12864-018-4724-8 | Genomic Island, Eukaryote, K-mer | Absent (May 01 2026) | |
| SalmonTE | https://doi.org/10.1142/9789813235533_0016 | RNA-Seq, Expression, NGS/HTS, Homology | Present (May 01 2026) | |
| SatDNA Analyzer | https://doi.org/10.1093/bioinformatics/btm005 | Simple Sequence Repeat/Microsatellite, Alignment, Library Generation | Present (May 01 2026) | |
| SciRoKo | https://doi.org/10.1093/bioinformatics/btm157 | Simple Sequence Repeat/Microsatellite, Summary, Annotation | Present (May 01 2026) | |
| Signature.py | https://doi.org/10.1007/978-1-4939-0931-5_12 | Small RNA, piRNA, NGS/HTS | Present (May 01 2026) | |
| SimulaTE | https://doi.org/10.1093/bioinformatics/btx772 | Simulation, Genome, NGS/HTS, Genotype, Polymorphism | Present (May 01 2026) | |
| SoftSV | https://doi.org/10.1093/bib/bbv028 | Structural Variation, Paired-End | Present (May 01 2026) | |
| SoftSearch | https://doi.org/10.1371/journal.pone.0083356 | Structural Variation, NGS/HTS, Short Read, Paired-End | ||
| SoloTE | https://doi.org/10.1038/s42003-022-04020-5 | RNA-Seq, Expression, Transcription, Single-Cell, NGS/HTS | Present (May 01 2026) | |
| Sputnik | https://doi.org/10.1038/ng822 | Simple Sequence Repeat/Microsatellite | Absent (May 01 2026) | |
| StainedGlass | https://doi.org/10.1093/bioinformatics/btac018 | Link | Simple Sequence Repeat/Microsatellite, Tandem Repeat, Visualization | Present (May 01 2026) |
| SyRI | https://doi.org/10.1186/s13059-019-1911-0 | Structural Variation, NGS/HTS, Comparative, Whole Genome | Present (May 01 2026) | |
| T-REKS | https://doi.org/10.1093/bioinformatics/btp482 | Tandem Repeat | Absent (May 01 2026) | |
| T-lex | https://doi.org/10.1093/nar/gkq1291 | Genotype, Polymorphism, NGS/HTS | Absent (May 01 2026) | |
| T-lex2 | https://doi.org/10.1093/nar/gku1250 | Genotype, Polymorphism, NGS/HTS | Present (May 01 2026) | |
| T-lex3 | https://doi.org/10.1093/bioinformatics/btz727 | Genotype, Polymorphism, NGS/HTS | Present (May 01 2026) | |
| T3E | https://doi.org/10.1186/s13100-022-00285-z | ChIP-Seq, NGS/HTS | Present (May 01 2026) | |
| TANGRAM | https://doi.org/10.1186/1471-2164-15-795 | Polymorphism, Genotype, NGS/HTS | Present (May 01 2026) | |
| TAPDANCE | https://doi.org/10.1186/1471-2105-13-154 | Genotype, Polymorphism, NGS/HTS | Present (May 01 2026) | |
| TAPO | https://doi.org/10.1016/j.febslet.2015.08.025 | Tandem Repeat, Web Server | Absent (May 01 2026) | |
| TARDIS | http://dx.doi.org/10.1016/j.ymeth.2017.05.030 | Structural Variation, NGS/HTS | Present (May 01 2026) | |
| TARGeT (Tree Analysis of Related Genes and Transposons) | https://doi.org/10.1093/nar/gkp295 | Homology, Web Server | Absent (May 01 2026) | |
| TASR | https://doi.org/10.1093/nar/gkv257 | Small RNA, Annotation | Present (May 01 2026) | |
| TCF | https://doi.org/10.1371/journal.pcbi.0030137 | Nested Insertion, Annotation, Web Server | Absent (May 01 2026) | |
| TE (Insertion/Deletion Dynamics for Transposable Elements) | https://doi.org/10.1534/genetics.118.301198 | Indel, Insertion Time, LTR Retrotransposon, Aegilops | Present (May 01 2026) | |
| TE Displayer | https://doi.org/10.1093/bioinformatics/btq639 | TE Display | Present (May 01 2026) | |
| TE transcripts | https://doi.org/10.1093/bioinformatics/btv422 | Expression, Transcription, RNA-Seq | Present (May 01 2026) | |
| TE-Aid | https://doi.org/10.1186/s13100-021-00259-7 | Annotation, Classification, Manual Curation, TE Libraries QC | Present (May 01 2026) | |
| TE-Learner | https://doi.org/10.1371/journal.pcbi.1006097 | Machine Learning, LTR Retrotransposon, Classification | Absent (May 01 2026) | |
| TE-Seq | https://doi.org/10.1101/2024.10.11.617912 | Annotation, RNA-Seq, Transcription, Expression | Present (May 01 2026) | |
| TE-Tracker | https://doi.org/10.1186/s12859-014-0377-z | Polymorphism, Genotype | Present (May 01 2026) | |
| TE-greedy-nester | https://doi.org/10.1093/bioinformatics/btaa632 | Link | Nested Insertion, LTR Retrotransposon | Present (May 01 2026) |
| TE-invasion-simulations | https://doi.org/10.1093/gbe/evy218 | Simulation, Genome, Evolution | Present (May 01 2026) | |
| TE-locate | https://doi.org/10.3390/biology1020395 | NGS/HTS, Paired-End, Genotype, Polymorphism | Present (May 01 2026) | |
| TE-nester | https://ieeexplore.ieee.org/document/8621071 | Structure, Nested Insertion | Present (May 01 2026) | |
| TE-reX | https://doi.org/10.1101/2020.07.02.163816 | Genotype, Polymorphism, Recombination | Present (May 01 2026) | |
| TEA | https://doi.org/10.1126/science.1222077 | Genotype, Polymorphism | Absent (May 01 2026) | |
| TEBreak | https://doi.org/10.1186/s13100-016-0076-6 | Genotype, Polymorphism, NGS/HTS | Present (May 01 2026) | |
| TECDetec | https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.718854 | Expression, Transcription, Chimera, NGS/HTS | Present (May 01 2026) | |
| TECookbook | https://doi.org/10.1093/nargab/lqad078 | ChIP-Seq, NGS/HTS, Analysis | Present (May 01 2026) | |
| TEF (Transposable Element Finder) | https://doi.org/10.1186/s12859-022-05011-3 | Polymorphism, Genotype, NGS/HTS | Present (May 01 2026) | |
| TEFLoN | https://doi.org/10.1093/gbe/evx050 | Annotation, Classification, NGS/HTS, Polymorphism, Genotype, Paired-End, Illumina | Present (May 01 2026) | |
| TEGRiP | https://doi.org/10.1101/2021.02.25.432867 | Eukaryotic Transposon, Annotation, Gene | Present (May 01 2026) | |
| TELR | NGS/HTS, PacBio, Oxford Nanopore, Long Read, Genotype, Polymorphism | Present (May 01 2026) | ||
| TEMP | https://doi.org/10.1093/nar/gku323 | Genotype, Polymorphism, NGS/HTS | Present (May 01 2026) | |
| TEMP2 | https://doi.org/10.1093/nar/gkab010 | Genotype, Polymorphism, NGS/HTS, Short Read | Present (May 01 2026) | |
| TEPEAK | https://doi.org/10.1101/2023.10.13.562297 | Genotype, Polymorphism, NGS/HTS | Present (May 01 2026) | |
| TEPID | https://doi.org/10.7554/eLife.20777.001 | Polymorphism, Genotype, NGS/HTS | Present (May 01 2026) | |
| TERAD | https://doi.org/10.1111/1755-0998.13080 | RAD-Seq, Repeat Masking, Annotation | Present (May 01 2026) | |
| TERL | https://doi.org/10.1093/bib/bbaa185 | Classification, Neural Network | Present (May 01 2026) | |
| TESD | https://doi.org/10.1093/bioinformatics/btl454 | Simulation, Genome | Absent (May 01 2026) | |
| TESeeker | https://doi.org/10.1186/1471-2105-12-130 | Homology, VirtualBox, Library Generation | Absent (May 01 2026) | |
| TETyper | https://doi.org/10.1099/mgen.0.000232 | Short Read, Paired-End, Polymorphism, Genotype, Archaea, Bacteria | Present (May 01 2026) | |
| TE_Density | https://doi.org/10.1186/s13100-022-00264-4 | Annotation, Analysis | Present (May 01 2026) | |
| TE_Discovery | https://doi.org/10.1101/701888 | Homology, Library Generation, Annotation, Analysis | Present (May 01 2026) | |
| TEcandidates | https://doi.org/10.1093/bioinformatics/bty423 | Expression, Transcription, RNA-Seq | Present (May 01 2026) | |
| TEclass | https://doi.org/10.1093/bioinformatics/btp084 | Classification | Present (May 01 2026) | |
| TEclass2 | https://doi.org/10.1101/2023.10.13.562246 | Classification, Web Server | Present (May 01 2026) | |
| TEffectR | https://doi.org/10.7717/peerj.8192 | RNA-Seq, Expression, NGS/HTS, Homology, Annotation | Present (May 01 2026) | |
| TEfinder | https://doi.org/10.3390/genes12020224 | Polymorphism, Genotype, NGS/HTS | Present (May 01 2026) | |
| TEgenomeSimulator | https://doi.org/10.64898/2026.03.09.710711 | A tool to simulate TE mutation and insertion into a random-synthesised or user-provided genome | Present (June 05 2026) | |
| TElocal | Expression, Transcription, RNA-Seq | Present (May 01 2026) | ||
| TEmarker | https://doi.org/10.1016/j.xplc.2021.100270 | Genotype, Polymorphism, NGS/HTS | Present (May 01 2026) | |
| 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 (May 01 2026) | |
| TEpeaks | ChIP-Seq | Present (May 01 2026) | ||
| TEsmall | https://doi.org/10.3389/fgene.2018.00461 | NGS/HTS, Small RNA, piRNA, Annotation | Present (May 01 2026) | |
| TEsorter | https://doi.org/10.1093/hr/uhac017 | Link | Classification, HMM | Present (May 01 2026) |
| TEspeX | https://doi.org/10.1093/bioinformatics/btac526 | Zenodo | NGS/HTS, Abundance, Expression, Transcription | Present (May 01 2026) |
| TEvarSim | https://doi.org/10.1371/journal.pcbi.1013933 | genome simulation tool for generating polymorphic transposable element (TE) variants | Present (June 05 2026) | |
| TIDAL | https://doi.org/10.1093/nar/gkv1193 | Genotype, Polymorphism, Illumina, Drosophila | Present (May 01 2026) | |
| TIDDIT | https://f1000research.com/articles/6-664/v2 | Rearrangement, NGS/HTS, Structural Variation | Present (May 01 2026) | |
| TIDK (Telomere Identifcation toolKit) | Github | De Novo, Telomere, Visualization | Present (May 01 2026) | |
| TIF (Transposon Insertion Finder) | https://doi.org/10.1186/1471-2105-15-71 | NGS/HTS, Genotype, Polymorphism, Short Read | Present (May 01 2026) | |
| TIGER (Target Integrative Genetic Element Retriever) | https://doi.org/10.1093/nar/gkaa156 | ICE/Integrative and Conjugative Element, Prophage/Bacteriophage | Present (May 01 2026) | |
| TIP_finder | https://doi.org/10.3390/biology9090281 | NGS/HTS, Genotype, Polymorphism | Present (May 01 2026) | |
| TIPseq-Hunter | https://doi.org/10.1073/pnas.1619797114 | Paired-End, Illumina, Machine Learning | Present (May 01 2026) | |
| TIR-Finder | https://doi.org/10.4137/EBO.S10619 | ITR/TIR/DNA Transposon, Web Server, Homology, Structure | Present (May 01 2026) | |
| TIR-Learner | https://doi.org/10.1016/j.molp.2019.02.008 | ITR/TIR/DNA Transposon, Homology, Structure, Annotation | Present (May 01 2026) | |
| TIRMITE | MITE, HMM, ITR/TIR/DNA Transposon, Annotation | Present (May 01 2026) | ||
| TLDR | https://doi.org/10.1101/2020.05.24.113068 | NGS/HTS, Long Read, Genotype, Polymorphism | ||
| TRACKPOSON | https://doi.org/10.1038/s41467-018-07974-5 | Genotype, Polymorphism, Paired-End, NGS/HTS | Absent (May 01 2026) | |
| TRANSIT | https://doi.org/10.1371/journal.pcbi.1004401 | Tn-Seq, Transposon Mutagenesis | Present (May 01 2026) | |
| TRANSPO | ITR/TIR/DNA Transposon, Homology | Absent (May 01 2026) | ||
| TRANScendence | https://doi.org/10.1186/s12859-017-1824-4 | De Novo, Homology, Structure, Library Generation, Annotation, Web Server | Present (May 01 2026) | |
| 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 (May 01 2026) | |
| TRF | https://doi.org/10.1093/nar/27.2.573 | Tandem Repeat | Present (May 01 2026) | |
| TRGT (Tandem Repeat Genotyping Tool) | https://doi.org/10.1101/2023.05.12.540470 | Tandem Repeat, PacBio, Long Read, NGS/HTS, Genotype | Present (May 01 2026) | |
| TROLL | https://doi.org/10.1093/bioinformatics/18.4.634 | Tandem Repeat | Present (May 01 2026) | |
| TRTools | https://doi.org/10.1101/2020.03.17.996033 | Tandem Repeat, Genotype | Present (May 01 2026) | |
| TRcaller | https://doi.org/10.1101/2023.02.15.528687 | Tandem Repeat, NGS/HTS, Long Read, Short Read | Absent (May 01 2026) | |
| TRiCoLOR | https://doi.org/10.1093/gigascience/giaa101 | Tandem Repeat, NGS/HTS, Long Read | Present (May 01 2026) | |
| TSDFinder | https://doi.org/10.1186/gb-2002-3-10-research0052 | LINE1, LINE/Non-LTR Retrotransposon, Target Site Duplication | Absent (May 01 2026) | |
| Tallymer | https://doi.org/10.1186/1471-2164-9-517 | K-mer Counting | Present (May 01 2026) | |
| Tandem Repeat Annotation Library | https://doi.org/10.1093/bioinformatics/btv306 | Tandem Repeat, Annotation | Absent (May 01 2026) | |
| TandemTools | https://doi.org/10.1093/bioinformatics/btaa440 | Tandem Repeat, Long Read, NGS/HTS, Assembly Polishing, Read Mapping | Present (May 01 2026) | |
| TeXP | https://doi.org/10.1371/journal.pcbi.1007293 | Expression, Transcription, RNA-Seq, NGS/HTS, LINE/Non-LTR Retrotransposon, Activity, Short Read | Present (May 01 2026) | |
| Tedna | https://doi.org/10.1093/bioinformatics/btu365 | Assembly, Illumina, Paired-End, NGS/HTS | Present (May 01 2026) | |
| Telescope | https://doi.org/10.1371/journal.pcbi.1006453 | Expression, Transcription, RNA-Seq | Present (May 01 2026) | |
| The RIPper | https://doi.org/10.7717/peerj.7447 | Link | RIP/Repeat-Induced Point Mutation, Mutation, GC, Repeat, Web Server | Present (May 01 2026) |
| TideHunter | https://doi.org/10.1093/bioinformatics/btz376 | Long Read, Tandem Repeat, NGS/HTS | Present (May 01 2026) | |
| TinT (Transposition in Transposition) | https://doi.org/10.1186/1471-2148-10-376 | Nested Insertion, Web Server | Present (May 01 2026) | |
| Tinscan | Comparative, Polymorphism, Genotype | Present (May 01 2026) | ||
| Tn-Core | https://doi.org/10.1021/acssynbio.8b00432 | Tn-Seq, Transposon Mutagenesis, RNA-Seq, Metabolic Modelling | Present (May 01 2026) | |
| Tn-seq Explorer | https://doi.org/10.1371/journal.pone.0126070 | Tn-Seq, Transposon Mutagenesis | Present (May 01 2026) | |
| Tn3+TA_finder | https://doi.org/10.1128/mBio.00452-20 | Transposon, Toxin-Antitoxin Loci | Present (May 01 2026) | |
| Tn3_finder | https://doi.org/10.1128/mBio.00452-20 | Transposon | Absent (May 01 2026) | |
| TnComp_finder | Composite Transposon | Absent (May 01 2026) | ||
| TnPred | http://dx.doi.org/10.1155/2012/678761 | Web Server, Transposase, Archaea, Bacteria, IS Element | Present (May 01 2026) | |
| TopHat-Fusion | https://doi.org/10.1186/gb-2011-12-8-r72 | RNA-Seq, Transcription, Expression, Fusion | Present (May 01 2026) | |
| TrEMOLO | https://doi.org/10.1101/2022.07.21.500944 | NGS/HTS, Long Read, Oxford Nanopore, Genotype, Polymorphism | Present (May 01 2026) | |
| TraDIS toolkit | https://doi.org/10.1093/bioinformatics/btw022 | Tn-Seq, Transposon Mutagenesis | Present (May 01 2026) | |
| TraFIC | https://doi.org/10.1126/science.1251343 | NGS/HTS, Paired-End, Homo sapiens, Genotype, Polymorphism | Present (May 01 2026) | |
| TranSurVeyor | https://doi.org/10.1093/nar/gky685 | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (May 01 2026) | |
| TranspoScope | https://doi.org/10.1093/bioinformatics/btaa244 | Genotype, Polymorphism, Visualization, NGS/HTS | Present (May 01 2026) | |
| Transposeq | https://doi.org/10.1101/gr.163659.113 | Polymorphism, Genotype, Web Server, Homo sapiens, Eukaryotic Retrotransposon | Absent (May 01 2026) | |
| Transposome | https://doi.org/10.1093/bioinformatics/btv059 | De Novo, Assembly, Homology | Present (May 01 2026) | |
| Transposon Cluster Finder | https://doi.org/10.1371/journal.pcbi.0030137 | Nested Insertion | Absent (May 01 2026) | |
| TransposonPSI | BLAST, Eukaryotic Transposon | Present (May 01 2026) | ||
| TransposonUltimate | https://doi.org/10.1093/nar/gkac136 | Link | Eukaryotic Transposon, Library Generation, Classification, Annotation, Structural Variation | Present (May 01 2026) |
| TrustTEr | https://doi.org/10.1101/2020.07.07.191668 | RNA-Seq, Expression | ||
| TypeTE | https://doi.org/10.1093/nar/gkaa074 | Genotype, Polymorphism | Present (May 01 2026) | |
| UCSC Repeat Browser | https://doi.org/10.1101/429613 | Repeat, Visualization, Annotation | Present (May 01 2026) | |
| ULTRA | https://doi.org/10.1145/3233547.3233604 | Tandem Repeat, HMM, Repeat Masking | Present (May 01 2026) | |
| V-ELMpiRNAPred | https://doi.org/10.1142/S0219720016500463 | piRNA, Neural Network | Absent (May 01 2026) | |
| VHICA | https://doi.org/10.1093/molbev/msv341 | Horizontal Transfer | Present (May 01 2026) | |
| VISMapper | https://doi.org/10.1186/s12859-017-1837-z | Virus, NGS/HTS, Web Server, Genotype, Polymorphism, Insertion Site, Visualization | Absent (May 01 2026) | |
| VRprofile | https://doi.org/10.1093/bib/bbw141 | Virulence, AMR/Antibiotic Resistance | Present (May 01 2026) | |
| VRprofile2 | https://doi.org/10.1093/nar/gkac321 | Virulence, AMR/Antibiotic Resistance | Present (May 01 2026) | |
| VariationHunter | https://doi.org/10.1093/bioinformatics/btq216 | NGS/HTS, Genotype, Polymorphism, Homo sapiens | ||
| VirSorter | https://doi.org/10.7717/peerj.985 | Prophage/Bacteriophage, Homology, HMM | Present (May 01 2026) | |
| VirusSeq | https://doi.org/10.1093/bioinformatics/bts665 | Virus, RNA-Seq, Homo sapiens | Present (May 01 2026) | |
| VirusTaxo | https://doi.org/10.1101/2021.04.29.442004 | Virus, K-mer, Classification, Web Server | Present (May 01 2026) | |
| VisualRepbase | https://doi.org/10.1186/1471-2105-9-345 | Annotation, Visualization | Present (May 01 2026) | |
| VisualTE | https://doi.org/10.1186/s12864-015-1351-5 | Annotation, Visualization | ||
| Vmatch | Repeat Annotation | Present (May 01 2026) | ||
| WGSSAT | https://doi.org/10.1093/jhered/esx075 | Simple Sequence Repeat/Microsatellite, Repeat Annotation, Primer | Present (May 01 2026) | |
| WindowMasker | https://doi.org/10.1093/bioinformatics/bti774 | Repeat Masking, Annotation, De Novo | Present (May 01 2026) | |
| Winnowmap2 | https://doi.org/10.1101/2020.11.01.363887 | Long Read, NGS/HTS, Repeat | Present (May 01 2026) | |
| WtP (What the Phage) | https://doi.org/10.1101/2020.07.24.219899 | Prophage/Bacteriophage, Annotation, Classification, Pipeline | Present (May 01 2026) | |
| YASS | https://doi.org/10.1093/nar/gki478 | Dot Plot, Visualization, Alignment, Web Server | Present (May 01 2026) | |
| YORO | https://doi.org/10.1371/journal.pone.0291925 | Classification, LTR Retrotransposon, Convolutional Neural Network | Present (May 01 2026) | |
| Zisland Explorer | https://doi.org/10.1093/bib/bbw019 | Genomic Island, GC | Absent (May 01 2026) | |
| alu-detect | https://doi.org/10.1093/nar/gkt612 | Alu, SINE, Genotype, Polymorphism, NGS/HTS, Paired-End | Present (May 01 2026) | |
| atena | http://52.71.54.154/packages/devel/bioc/html/atena.html | Pipeline, Expression, Transcription, RNA-Seq | Present (May 01 2026) | |
| binary_plus_multi_clasification.py | https://doi.org/10.7717/peerj.11456 | Classification, LTR Retrotransposon, K-mer | Present (May 01 2026) | |
| breseq | https://doi.org/10.1186/1471-2164-15-1039 | Structural Variation, Polymorphism, Genotype | Absent (May 01 2026) | |
| collapse_RepeatMasker_annotation | https://doi.org/10.1007/978-1-0716-2380-0_21 | Annotation | Present (May 01 2026) | |
| de_novo-identification | https://doi.org/10.13140/RG.2.2.27068.69765 | De Novo, Eukaryotic Transposon | Present (May 01 2026) | |
| detectIR | https://doi.org/10.1371/journal.pone.0113349 | Inverted Repeat | Present (May 01 2026) | |
| detectMITE | https://doi.org/10.1038/srep19688 | Library Generation, MITE, ITR/TIR/DNA Transposon | Present (May 01 2026) | |
| detettore | https://doi.org/10.1111/nph.16308 | Polymorphism, Genotype, NGS/HTS, Paired-End | Present (May 01 2026) | |
| digIS | https://doi.org/10.1186/s12859-021-04177-6 | IS Element, HMM | Present (May 01 2026) | |
| dimorphicERV | https://doi.org/10.1186/s13100-018-0142-3 | NGS/HTS, Short Read, Genotype, Polymorphism, ERV/Endogenous Retrovirus | Present (May 01 2026) | |
| discord-retro | https://arxiv.org/abs/1501.04268 | Illumina, Paired-End, NGS/HTS, Polymorphism, Genotype | Present (May 01 2026) | |
| dnaPipeTE | https://doi.org/10.1093/gbe/evv050 | GitHub | NGS/HTS, Assembly, Annotation | Present (May 01 2026) |
| dnaasm | https://doi.org/10.7490/f1000research.1114626.1 | Repeat, NGS/HTS, De Novo | Present (May 01 2026) | |
| dotmatcher | http://embossgui.sourceforge.net/demo/manual/dotmatcher.html | Dot Plot, Visualization | Present (May 01 2026) | |
| dotplot | Dot Plot, Visualization | Present (May 01 2026) | ||
| geNomad | https://doi.org/10.1038/s41587-023-01953-y | Virus, Plasmid, Machine Learning, Detection, Classification | Present (May 01 2026) | |
| iMGEins | https://doi.org/10.1186/s12864-018-5290-9 | NGS/HTS, Paired-End, Homology, Genotype, Polymorphism, Annotation | Present (May 01 2026) | |
| iMSAT | https://doi.org/10.1186/1471-2164-15-858 | Simple Sequence Repeat/Microsatellite, Illumina, NGS/HTS, Short Read, Genotype, Polymorphism, Repeat Extraction | Present (May 01 2026) | |
| iMapper | https://doi.org/10.1093/bioinformatics/btn541 | Genome, Ensembl, Transposon Mutagenesis | Present (May 01 2026) | |
| iSVP | https://doi.org/10.1186/1752-0509-7-s6-s8 | Structural Variation, Pipeline | Present (May 01 2026) | |
| inGAP-sv | https://doi.org/10.1093/nar/gkr506 | Structural Variation, NGS/HTS, Bayesian, Paired-End, Visualization | Present (May 01 2026) | |
| ltr.pl | https://doi.org/10.1186/1471-2164-8-90 | De Novo, LTR Retrotransposon, HMM | Absent (May 01 2026) | |
| mSINGS | https://doi.org/10.1373/clinchem.2014.223677 | Simple Sequence Repeat/Microsatellite, Instability, Polymorphism, Genotype, NGS/HTS, Cancer | Present (May 01 2026) | |
| 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 | Present (May 01 2026) |
| mge-cluster | https://doi.org/10.1101/2022.12.16.520696 | Link | Plasmid, Classification | Present (May 01 2026) |
| micRocounter | https://doi.org/10.1534/g3.119.400335 | Simple Sequence Repeat/Microsatellite, Annotation | Present (May 01 2026) | |
| mosaicFlye | https://doi.org/10.1101/2020.01.15.908285 | NGS/HTS, Long Read, Mosaic Repeat, Segmental Duplication, Assembly | Present (May 01 2026) | |
| mreps | https://doi.org/10.1093/nar/gkg617 | Tandem Repeat, De Novo, Library Generation | Present (May 01 2026) | |
| msatcommander | https://doi.org/10.1111/j.1471-8286.2007.01884.x | Simple Sequence Repeat/Microsatellite, Primer | Present (May 01 2026) | |
| msatfinder | Link | Simple Sequence Repeat/Microsatellite, Primer, Annotation, Repeat Extraction | Present (May 01 2026) | |
| nanomonsv | https://doi.org/10.1101/2020.07.22.214262 | Structural Variation, NGS/HTS, Long Read, Cancer | Present (May 01 2026) | |
| nanotei | https://doi.org/10.3390/plants10122681 | NGS/HTS, Oxford Nanopore, Polymorphism, Genotype | Present (May 01 2026) | |
| ncRNAclassifier | https://doi.org/10.1186/1471-2105-13-246 | ncRNA, miRNA | Absent (May 01 2026) | |
| nf-repeatmasking | http://doi.org/10.5281/zenodo.1134750 | Repeat Masking, Classification | Present (May 01 2026) | |
| ngs_te_mapper | https://doi.org/10.1371/journal.pone.0030008 | Target Site Duplication, Homology, NGS/HTS | Present (May 01 2026) | |
| ntHits | https://doi.org/10.1371/journal.pone.0030008 | K-mer, Repeat | Present (May 01 2026) | |
| oriTfinder | https://doi.org/10.1093/nar/gky352 | Origin of Transfer, Plasmid, ICE/Integrative and Conjugative Element | Present (May 01 2026) | |
| packFinder | https://doi.org/10.1101/2021.06.18.448592 | Link | ITR/TIR/DNA Transposon, MuDR/Mutator, Pack-MULE | Present (May 01 2026) |
| panGRP | https://doi.org/10.1093/bioinformatics/btaa792 | Genomic Island | Present (May 01 2026) | |
| panHiTE | https://doi.org/10.1101/2025.02.15.638472 | Insertion Polymorphism, Polymorphism, Pangenome | Present (May 01 2026) | |
| panISa | https://doi.org/10.1093/bioinformatics/bty479 | De Novo, IS Element, NGS/HTS, Short Read, Annotation, Homology | Present (May 01 2026) | |
| phRAIDER | https://doi.org/10.1093/bioinformatics/btw258 | De Novo, Library Generation | Present (May 01 2026) | |
| piPipes | https://doi.org/10.1093/bioinformatics/btu647 | piRNA, RNA-Seq, ChIP-Seq, NGS/HTS | Present (May 01 2026) | |
| piRNA Pipeline | https://doi.org/10.1093/nar/gky761 | piRNA, NGS/HTS | Present (May 01 2026) | |
| piRNAPredictor | https://doi.org/10.1186/s12859-016-1206-3 | piRNA, Prediction | Present (May 01 2026) | |
| piRNN | https://doi.org/10.7717/peerj.5429 | piRNA, K-mer, Convolutional Neural Network | Present (May 01 2026) | |
| piRPred | https://doi.org/10.1093/bioinformatics/btu441 | piRNA, SVM | Absent (May 01 2026) | |
| 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 (May 01 2026) | |
| polymorphicHERV | https://doi.org/10.1371/journal.pcbi.1006564 | ERV/Endogenous Retrovirus, K-mer, Genotype, Polymorphism, NGS/HTS | Present (May 01 2026) | |
| proTRAC | https://doi.org/10.1186/1471-2105-13-5 | piRNA | Absent (May 01 2026) | |
| rCANID | https://doi.org/10.1109/TNB.2019.2908438 | Long Read, NGS/HTS, Genotype, Polymorphism, Structural Variation | Present (May 01 2026) | |
| rMETL | https://doi.org/10.1093/bioinformatics/btz106 | Long Read, NGS/HTS, Genotype, Polymorphism | Present (May 01 2026) | |
| rMFilter | https://doi.org/10.1093/bioinformatics/btx279 | NGS/HTS, Structural Variation, Long Read | Present (May 01 2026) | |
| rTea (RNA-based Transposable Element Analyzer) | https://doi.org/10.1101/2023.10.16.562422 | RNA-Seq, Transcription, Expression, Fusion | Present (May 01 2026) | |
| rampage_alu | https://doi.org/10.1101/gr.249789.119 | RNA-Seq, Expression, Alu, SINE, RAMPAGE, NGS/HTS, Paired-End | Present (May 01 2026) | |
| read2marker | https://doi.org/10.2144/000112025 | Simple Sequence Repeat/Microsatellite, Primer | ||
| regulaTER | https://doi.org/10.1016/j.jmb.2024.168887 | Expression, Transcription | Present (May 01 2026) | |
| repeatR | Eukaryotic Transposon, RepeatMasker, Annotation, Summary | Present (May 01 2026) | ||
| reputils | Github | TE Identification, Alignment, MSA, Manual Curation | Present (May 01 2026) | |
| retroSeeker | https://doi.org/10.1007/s44307-023-00005-5 | Eukaryotic Retrotransposon, Detection, Homology | Present (May 01 2026) | |
| retrotransposons-spread | https://doi.org/10.1093/bioinformatics/btw622 | Simulation, LTR Retrotransposon | Present (May 01 2026) | |
| sRNAPipe | https://doi.org/10.1186/s13100-018-0130-7 | Small RNA, RNA-Seq, Annotation | Present (May 01 2026) | |
| sRNAplot | https://doi.org/10.1038/s41559-017-0403-4 | Small RNA, piRNA, Visualization | Present (May 01 2026) | |
| sTELLeR | https://doi.org/10.1093/bioinformatics/btae686 | Long Read, Insertion Polymorphism, Polymorphism | Present (May 01 2026) | |
| scTE | https://doi.org/10.1038/s41467-021-21808-x | Single-Cell, RNA-Seq, Expression, Eukaryotic Transposon | Present (May 01 2026) | |
| sideRETRO | https://doi.org/10.1101/2020.03.09.983858 | Pseudogene, CNV/Copy Number Variation, Genotype, Polymorphism, NGS/HTS | Present (May 01 2026) | |
| sompop | https://doi.org/10.1093/bioinformatics/btaa279 | LINE1, LINE/Non-LTR Retrotransposon, Simulation, Cancer | Present (May 01 2026) | |
| somrit | https://www.biorxiv.org/content/10.1101/2023.08.06.552193v2.full.pdf | Retrotransposon, Insertion Polymorphism, Somatic, Mosaicism | Present (May 01 2026) | |
| starfish | https://doi.org/10.1101/2023.10.24.563810 | Starship, Tyrosine Recombinase, Detection, Annotation | Present (May 01 2026) | |
| svaRetro | https://doi.org/10.46471/gigabyte.70 | Structural Variation, Pseudogene, Expression, Transcription, LINE/Non-LTR Retrotransposon | Present (May 01 2026) | |
| svclassify | https://doi.org/10.1186/s12864-016-2366-2 | Structural Variation, Clustering, Classification | Present (May 01 2026) | |
| svviz2 | https://doi.org/10.1093/bioinformatics/btv478 | Structural Variation, Visualization | Present (May 01 2026) | |
| tRNA-DL | https://doi.org/10.1159/000493215 | tRNA, Deep Neural Network | ||
| tRNAscan-SE- On-line | https://doi.org/10.1093/nar/gkw413 | Link | tRNA | Absent (May 01 2026) |
| tantan | https://doi.org/10.1093/nar/gkq1212 | Repeat, Repeat Masking | Present (May 01 2026) | |
| tek2 | https://doi.org/10.1093/molbev/msz220 | Simulation, Genome, Divergence, Evolution | Present (May 01 2026) | |
| tephra | Homology, Library Generation, Structure, Classification, Age, Annotation | Present (May 01 2026) | ||
| vHULK (Viral Host UnveiLing Kit) | https://doi.org/10.1101/2020.12.06.413476 | Prophage/Bacteriophage | Present (May 01 2026) | |
| xTea | https://doi.org/10.1038/s41467-021-24041-8 | Eukaryotic Transposon, Polymorphism, Genotype, Long Read, Short Read, Pangenome | Present (May 01 2026) | |
| xenoGI | https://doi.org/10.1186/s12859-018-2038-0 | Genomic Island, Synteny, Phylogeny | Present (May 01 2026) |