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 (Dec 01 2025) | |
| 2lpiRNApred | https://doi.org/10.1080/15476286.2020.1734382 | piRNA | Present (Dec 01 2025) | |
| 4-LIN | https://doi.org/10.1093/sysbio/syac082 | Web Server, Phylogeny, Eukaryotic Retrotransposon | Present (Dec 01 2025) | |
| AAARF (Assisted Automated Assembler of Repeat Families) | https://doi.org/10.1186/1471-2105-9-235 | Homology, Alignment | Present (Dec 01 2025) | |
| ANUBIS | https://doi.org/10.1093/nar/gkaa679 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism, Visualization | Present (Dec 01 2025) | |
| ARTIST | https://doi.org/10.1371/journal.pgen.1004782 | Tn-Seq, Transposon Mutagenesis, HMM | Present (Dec 01 2025) | |
| AgIn | https://doi.org/10.1093/bioinformatics/btw360 | PacBio, Methylation | Present (Dec 01 2025) | |
| AlbaTraDIS | https://doi.org/10.1371/journal.pcbi.1007980 | Tn-Seq, Transposon Mutagenesis | Present (Dec 01 2025) | |
| Alien_Hunter | https://doi.org/10.1093/bioinformatics/btl369 | Genomic Island, HMM | Absent (Dec 01 2025) | |
| Alpha-CENTAURI | https://doi.org/10.1093/bioinformatics/btw101 | Satellite, Centromere, Tandem Repeat, HMM, Long Read | Present (Dec 01 2025) | |
| AluMine | https://doi.org/10.1101/588434 | Alu, SINE, Genotype, Polymorphism, NGS/HTS | Present (Dec 01 2025) | |
| AnTE | https://doi.org/10.1371/journal.pgen.1004482 | Simulation, Phylogeny, Bayesian MCMC, Ancestral Reconstruction | Absent (Dec 01 2025) | |
| AnnoSINE | https://doi.org/10.1093/plphys/kiab524 | SINE, Annotation, HMM | Present (Dec 01 2025) | |
| AntiDefenseFinder | https://doi.org/10.1093/nar/gkae1171 | Link | Web Server, Anti-Defense System, Bacteria, Archaea, Prophage/Bacteriophage | Present (Dec 01 2025) |
| Attacca | https://doi.org/10.1186/1471-2105-10-281 | Integron | ||
| BERTE | https://doi.org/10.1101/2024.01.28.577612 | Classification | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| BacAnt | https://doi.org/10.3389/fmicb.2021.649969 | Link | IS Element, Archaeal/Bacterial Transposon, Integron, AMR/Antibiotic Resistance, Annotation, Web Server | Present (Dec 01 2025) |
| Bakta | https://doi.org/10.1099/mgen.0.000685 | Link | Metagenomics, Annotation | Present (Dec 01 2025) |
| 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 (Dec 01 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 (Dec 01 2025) | |
| CARP | https://doi.org/10.1371/journal.pone.0193588 | De Novo, Library Generation, Homology, Annotation | Present (Dec 01 2025) | |
| CAULIFINDER | https://doi.org/10.1186/s13100-022-00288-w | Detection, Annotation, EVE/Endogenous Viral Element, Plants, Virus | Present (Dec 01 2025) | |
| CAlu Alu Classifier | https://doi.org/10.1016/j.cell.2010.05.020 | Genotype, Polymorphism, Homo sapiens, Alu, SINE, Web Server | Absent (Dec 01 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 (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| CLARI-TE | https://doi.org/10.1186/s13059-014-0546-4 | Homology, Annotation, Nested Insertion | Present (Dec 01 2025) | |
| CLIFinder | https://doi.org/10.1093/bioinformatics/btx671 | LINE1, Transcription, RNA-Seq, Expression, Chimera, NGS/HTS | Present (Dec 01 2025) | |
| CLOVE | https://doi.org/10.1186/s12859-017-1760-3 | Structural Variation | Present (Dec 01 2025) | |
| ColabCuraTE | https://doi.org/10.1186/s13100-025-00389-2 | Manual Curation | Present (Dec 01 2025) | |
| COLOMBO | https://doi.org/10.1186/1471-2105-7-142 | Genomic Island, Codon Usage, HMM | Present (Dec 01 2025) | |
| CONJscan | https://doi.org/10.1007/978-1-4939-9877-7_19 | Plasmid, ICE/Integrative and Conjugative Element | Present (Dec 01 2025) | |
| COPLA | https://doi.org/10.1101/2020.12.15.422809 | Plasmid, Classification, Homology | Present (Dec 01 2025) | |
| COSEG | Subfamily Identification, Eukaryotic Transposon, Alu, SINE | Present (Dec 01 2025) | ||
| CRISPRCasTyper | https://doi.org/10.1101/2020.05.15.097824 | Link | CRISPR, Classification, Annotation | Present (Dec 01 2025) |
| Censor | https://doi.org/10.1016/S0097-8485(96)80013-1 | Annotation, Repeat Masking | Absent (Dec 01 2025) | |
| ChimeraTE | https://doi.org/10.1093/nar/gkad671 | RNA-Seq, Expression, Transcription, Paired-End, NGS/HTS, Chimera | Present (Dec 01 2025) | |
| ClassifyTE | https://doi.org/10.1093/bioinformatics/btab146 | Classification, Eukaryotic Transposon | Present (Dec 01 2025) | |
| ClustAGE | https://doi.org/10.1186/s12859-018-2154-x | Comparative, BLAST, Archaea, Bacteria | Present (Dec 01 2025) | |
| CompTIS | https://doi.org/10.1128/mSphere.00031-19 | Tn-Seq, Transposon Mutagenesis, PCA | Present (Dec 01 2025) | |
| ConTExt | https://genome.cshlp.org/content/28/5/714 | Illumina, Paired-End, Homology, NGS/HTS, Polymorphism | Present (Dec 01 2025) | |
| ConsensuSV | https://doi.org/10.1093/bioinformatics/btac709 | Structural Variation, Pipeline, Indel, Polymorphism | Present (Dec 01 2025) | |
| ConsensusSV | https://doi.org/10.1093/bioinformatics/btac709 | NGS/HTS, Short Read, Illumina, Structural Variation | Present (Dec 01 2025) | |
| D-Genies | https://doi.org/10.7717/peerj.4958 | Dot Plot, Visualization | Present (Dec 01 2025) | |
| DANTE | Link | Homology, Library Generation | Present (Dec 01 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 (Dec 01 2025) | |
| DARTS (Domain-Associated RetroTransposon Search) | https://doi.org/10.1101/2021.12.03.471067 | Pipeline, Homology, Annotation, Retrotransposon | Present (Dec 01 2025) | |
| DAWG-PAWS | https://doi.org/10.1186/1746-4811-5-8 | Homology, HMM, Annotation, Gene Prediction | Present (Dec 01 2025) | |
| DBSCAN-SWA | https://doi.org/10.1101/2020.07.12.199018 | Prophage/Bacteriophage, Homology | Present (Dec 01 2025) | |
| DD-Detection | https://doi.org/10.1093/bioinformatics/btv621 | NGS/HTS, Illumina, Paired-End, Polymorphism | Present (Dec 01 2025) | |
| DEPht | https://doi.org/10.1093/nar/gkac273 | Annotation, Extraction, Prophage/Bacteriophage | Present (Dec 01 2025) | |
| DGRscan | https://doi.org/10.3390/ijms150814234 | DGR/Diversity Generating Retroelement, Annotation | Present (Dec 01 2025) | |
| DIVE | https://doi.org/10.1101/2022.06.13.495703 | De Novo, K-mer, Repeat | Present (Dec 01 2025) | |
| DTExpress | https://doi.org/10.1007/978-1-0716-1134-0_2 | RNA-Seq, Expression | Present (Dec 01 2025) | |
| DarkHorse | https://doi.org/10.1186/gb-2007-8-2-r16 | Horizontal Transfer, Homology, Phylogeny | Present (Dec 01 2025) | |
| DeBreak | https://doi.org/10.21203/rs.3.rs-1261915/v1 | NGS/HTS, Long Read, Structural Variation | Present (Dec 01 2025) | |
| DeRIP | https://doi.org/10.1186/1471-2164-11-655 | RIP/Repeat-Induced Point Mutation, Prediction, Fungi | Present (Dec 01 2025) | |
| DeepMEI | https://doi.org/10.1101/2023.03.07.531451 | NGS/HTS, Short Read, Genotype, Polymorphism, Convolutional Neural Network | Present (Dec 01 2025) | |
| DeepRepeat | https://doi.org/10.1186/s13059-022-02670-6 | NGS/HTS, Short Tandem Repeat, Long Read, Oxford Nanopore | Present (Dec 01 2025) | |
| DeepTE | https://doi.org/10.1093/bioinformatics/btaa519 | Classification, Convolutional Neural Network | Present (Dec 01 2025) | |
| Delly | https://doi.org/10.1093/bioinformatics/bts378 | Structural Variation, NGS/HTS, Short Read, Paired-End | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| DiGReF | https://doi.org/10.1186/1471-2164-13-430 | DGR/Diversity Generating Retroelement, Annotation | Absent (Dec 01 2025) | |
| Dna-brnn | https://doi.org/10.1093/bioinformatics/btz264 | Satellite, Centromere, Neural Network | Present (Dec 01 2025) | |
| Domain Organizer | https://doi.org/10.1093/bioinformatics/btl337 | Alignment, HMM, Domain, Visualization | Absent (Dec 01 2025) | |
| Dotlet | https://doi.org/10.1093/bioinformatics/16.2.178 | Dot Plot, Visualization | Present (Dec 01 2025) | |
| Dotter | https://doi.org/10.1016/0378-1119(95)00714-8 | Visualization, Dot Plot | Present (Dec 01 2025) | |
| Duster | https://peercommunityjournal.org/articles/10.24072/pcjournal.68/ | Library Generation, Homology, K-mer | Present (Dec 01 2025) | |
| Dysgu | https://doi.org/10.1093/nar/gkac039 | NGS/HTS, Short Read, Long Read, Structural Variation | Present (Dec 01 2025) | |
| EAHelitron | https://doi.org/10.1186/s12859-019-2945-8 | Helitron, Structure | Present (Dec 01 2025) | |
| ECCsplorer | https://doi.org/10.1186/s12859-021-04545-2 | eccDNA, Identification, Active TEs | Present (Dec 01 2025) | |
| EDTA | https://doi.org/10.1186/s13059-019-1905-y | Library Generation, Filtering, Structure, De Novo | Present (Dec 01 2025) | |
| EGID | https://doi.org/10.6026/007/97320630007311 | Genomic Island, Prediction | Absent (Dec 01 2025) | |
| ELAN | https://doi.org/10.1093/nar/gkr337 | Homology, Insertion Site, Consensus | Absent (Dec 01 2025) | |
| ELITE (Efficiently Locating Insertions of Transposable Elements) | https://doi.org/10.1145/3307339.3342182 | Genotype, Polymorphism, NGS/HTS | Absent (Dec 01 2025) | |
| ERVcaller | https://doi.org/10.1093/bioinformatics/btz205 | ERV/Endogenous Retrovirus, Homo sapiens, NGS/HTS, Polymorphism, Genotype | Absent (Dec 01 2025) | |
| ERVmap | https://doi.org/10.1073/pnas.1814589115 | ERV/Endogenous Retrovirus, RNA-Seq, Transcriptome, Homo sapiens | Present (Dec 01 2025) | |
| ESAP Plus | https://doi.org/10.1186/s12864-016-3328-4 | Simple Sequence Repeat/Microsatellite, Expression, EST, Clustering, Repeat Masking | Absent (Dec 01 2025) | |
| ESMP | https://doi.org/10.6026/97320630008206 | Simple Sequence Repeat/Microsatellite, Expression, EST, Clustering | Absent (Dec 01 2025) | |
| ESSENTIALS | https://doi.org/10.1371/journal.pone.0043012 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Absent (Dec 01 2025) | |
| EVANGELIST | https://doi.org/10.3390/genes12020312 | GC, Repeat Annotation | Present (Dec 01 2025) | |
| EarlGrey | https://doi.org/10.21203/rs.3.rs-1812599/v1 | Pipeline, Annotation, Repeat Masking, Homology, De Novo, Library Generation | Present (Dec 01 2025) | |
| Easymap | https://doi.org/10.3389/fpls.2021.655286 | Link | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (Dec 01 2025) |
| Ecc_finder | https://www.frontiersin.org/articles/10.3389/fpls.2021.743742/abstract | essDNA, NGS/HTS, Oxford Nanopore | Present (Dec 01 2025) | |
| EpiTEome | https://doi.org/10.1186/s13059-017-1232-0 | Polymorphism, Genotype, NGS/HTS, Methyl-Seq, Bisulfite, Methylation, | Present (Dec 01 2025) | |
| ExoPLOT | https://doi.org/10.1016/j.ygeno.2022.110434 | RNA-Seq, Expression, Transcription, NGS/HTS | Present (Dec 01 2025) | |
| ExpansionHunter | https://doi.org/10.1101/gr.225672.117 | Short Read, NGS/HTS, Short Tandem Repeat | Present (Dec 01 2025) | |
| ExpansionHunter Denovo | https://doi.org/10.1101/863035 | Short Read, NGS/HTS, Short Tandem Repeat | Present (Dec 01 2025) | |
| ExplorATE | https://doi.org/10.1093/bioinformatics/btac354 | Expression, Transcription, RNA-Seq | Present (Dec 01 2025) | |
| FASTQINS | https://doi.org/10.1093/nar/gkaa679 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism, Read Mapping | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| Fastq2LoxDel | https://doi.org/10.1101/2020.07.14.202044 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (Dec 01 2025) | |
| FiTnEss (Finding Tn-Seq Essentials) | https://doi.org/10.1073/pnas.1900570116 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (Dec 01 2025) | |
| FindTelomeres | Telomere | Present (Dec 01 2025) | ||
| FishPi | https://doi.org/10.1186/s13100-025-00342-3 | piRNA | Present (Dec 01 2025) | |
| FlexDotPlot | https://doi.org/10.1101/2020.04.03.023655 | Visualization, Dot Plot | Present (Dec 01 2025) | |
| FlexiDot | https://doi.org/10.1093/bioinformatics/bty395 | Visualization, Dot Plot | Present (Dec 01 2025) | |
| FullSSR | https://doi.org/10.1155/2016/6040124 | Simple Sequence Repeat/Microsatellite, Primer | Present (Dec 01 2025) | |
| G-IMEx | https://doi.org/10.6026/97320630005221 | Simple Sequence Repeat/Microsatellite, Repeat Extraction, Annotation | Absent (Dec 01 2025) | |
| GASVPro | https://doi.org/10.1186/gb-2012-13-3-r22 | Structural Variation, NGS/HTS, Paired-End | Absent (Dec 01 2025) | |
| GC-Profile | https://doi.org/10.2174/1389202915999140328163125 | Genomic Island, GC | Absent (Dec 01 2025) | |
| GI-Cluster | https://doi.org/10.1142/S0219720018400103 | Genomic Island, GC, Codon Usage, K-mer | Present (Dec 01 2025) | |
| GI-POP | https://doi.org/10.1016/j.gene.2012.11.063 | Genomic Island, SVM, Annotation | Absent (Dec 01 2025) | |
| GI-SVM | https://doi.org/10.1142/S0219720016400035 | Genomic Island, SVM, K-mer | Present (Dec 01 2025) | |
| GIDetector | https://doi.org/10.1186/1471-2164-11-S2-S1 | Genomic Island, Pipeline | Absent (Dec 01 2025) | |
| GIHunter | https://doi.org/10.4172/jpb.1000322 | Genomic Island, Prediction | Absent (Dec 01 2025) | |
| GIPSy | https://doi.org/10.1016/j.jbiotec.2015.09.008 | Genomic Island, GC, Homology, HMM | Present (Dec 01 2025) | |
| GIST | https://doi.org/10.6026/97320630008203 | Genomic Island, Pipeline | Absent (Dec 01 2025) | |
| GIV | https://doi.org/10.6026/97320630009879 | Genomic Island, Visualization | Absent (Dec 01 2025) | |
| GMATA | https://doi.org/10.3389/fpls.2016.01350 | Simple Sequence Repeat/Microsatellite, Repeat Extraction, Annotation, Primer | Present (Dec 01 2025) | |
| GMATo | https://doi.org/10.6026/97320630009541 | Simple Sequence Repeat/Microsatellite, Repeat Annotation | Present (Dec 01 2025) | |
| GPAC (Genome Presence/Absence Compiler) | https://doi.org/10.1093/molbev/msu276 | Polymorphism, Genotype | Present (Dec 01 2025) | |
| GRASPER | https://doi.org/10.1089/cmb.2013.0129 | Structural Variation, Repeat, Homology, NGS/HTS, Paired-End | Present (Dec 01 2025) | |
| GREAM | https://doi.org/10.1371/journal.pone.0133647 | Mammal, Web Server, Genome, Analysis | Present (Dec 01 2025) | |
| GeIST | https://doi.org/10.1093/bioinformatics/btv350 | Tn-Seq, Transposon Mutagenesis | Present (Dec 01 2025) | |
| GeneTEFlow | https://doi.org/10.1101/2020.04.28.065862 | RNA-Seq, NGS/HTS, Nextflow | Present (Dec 01 2025) | |
| Generic Repeat Finder | https://doi.org/10.1104/pp.19.00386 | LTR Retrotransposon, MITE, Inverted Repeat, ITR/TIR/DNA Transposon | Present (Dec 01 2025) | |
| Genome ARTIST v2 | https://doi.org/10.3390/ijms232012686 | Tn-Seq, Transposon Mutagenesis, Drosophila, ITR/TIR/DNA Transposon | Present (Dec 01 2025) | |
| GenomeDelta | https://doi.org/10.1186/s13059-024-03459-5 | Polymorphism, Insertion Polymorphism, Short Read | Present (Dec 01 2025) | |
| GenomeDiff | Dot Plot, Visualization, Virus | Present (Dec 01 2025) | ||
| GenomeTools | https://doi.ieeecomputersociety.org/10.1109/TCBB.2013.68 | Genome Annotation | Present (Dec 01 2025) | |
| Gepard | https://doi.org/10.1093/bioinformatics/btm039 | Visualization, Dot Plot | Present (Dec 01 2025) | |
| GraffiTE | https://doi.org/10.1101/2023.09.11.557209 | Polymorphism, Structural Variation, Long Read, NGS/HTS, Assembly, Pangenome, Graph-Genome, Genotype | Present (Dec 01 2025) | |
| GraphTyper | https://doi.org/10.1038/ng.3964 | Structural Variation, Short Read, NGS/HTS | Present (Dec 01 2025) | |
| GraphTyper2 | https://doi.org/10.1038/s41467-019-13341-9 | Structural Variation, Short Read, NGS/HTS | Present (Dec 01 2025) | |
| Greedier | https://doi.org/10.1093/bioinformatics/btm613 | Homology, Repeat Masking, Nested Insertion, Graph | Present (Dec 01 2025) | |
| HDRSM (Highly Divergent Repeat Search Method) | https://doi.org/10.1186/s12859-021-03977-0 | SINE | Present (Dec 01 2025) | |
| HELIANO | https://doi.org/10.1101/2024.02.08.579435 | Helitron, Annotation | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| HMMER | https://doi.org/10.1371/journal.pcbi.1000069 | HMM | Present (Dec 01 2025) | |
| HTdetect | https://doi.org/10.1093/gbe/evu026 | Horizontal Transfer, Homology | Present (Dec 01 2025) | |
| HashRepeatFinder | https://doi.org/10.1007/s12539-015-0119-6 | De Novo, Library Generation | Absent (Dec 01 2025) | |
| HelSearch | https://doi.org/10.1073/pnas.0905563106 | Helitron, Structure | Present (Dec 01 2025) | |
| HelitronFinder | https://doi.org/10.1186/1471-2164-9-51 | Helitron, Structure | Absent (Dec 01 2025) | |
| HelitronScanner | https://doi.org/10.1073/pnas.1410068111 | Helitron, Structure | Present (Dec 01 2025) | |
| HiC-TE | https://doi.org/10.1101/2021.12.18.473300 | Hi-C, NGS/HTS, Pipeline | Present (Dec 01 2025) | |
| HiTE | https://doi.org/10.1101/2023.05.23.541879 | Detection, Annotation | Present (Dec 01 2025) | |
| HiTea | https://doi.org/10.1101/2020.04.27.060145 | Hi-C, NGS/HTS, Genotype, Polymorphism | Present (Dec 01 2025) | |
| HomologMiner | https://doi.org/10.1093/bioinformatics/btm048 | Homology, Genome, Comparative | Absent (Dec 01 2025) | |
| ICEfinder | https://doi.org/10.1093/nar/gky1123 | Link | ICE/Integrative and Conjugative Element, HMM | Absent (Dec 01 2025) |
| ICEscreen | https://doi.org/10.1093/nargab/lqac079 | ICE/Integrative and Conjugative Element, HMM | Present (Dec 01 2025) | |
| IDSSR | https://doi.org/10.3390/ijms20143497 | Simple Sequence Repeat/Microsatellite, NGS/HTS, Paired-End, Primer, Repeat Annotation, Polymorphism | Present (Dec 01 2025) | |
| IGIPT | https://doi.org/10.6026/007/97320630007307 | Genomic Island, Nucleotide Composition, Visualization | Present (Dec 01 2025) | |
| IMEx | https://doi.org/10.1093/bioinformatics/btm097 | Simple Sequence Repeat/Microsatellite, Annotation, Web Server | Absent (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| IRplus | https://doi.org/10.1093/gbe/evad177 | Link | Inverted Repeat, Plastid, Web Server | Present (Dec 01 2025) |
| ISAbR_finder | IS Element, AMR/Antibiotic Resistance | Absent (Dec 01 2025) | ||
| ISCompare | https://doi.org/10.1093/g3journal/jkab181 | IS Element, Genotype, Polymorphism | Present (Dec 01 2025) | |
| ISEScan | https://doi.org/10.1093/bioinformatics/btx433 | IS Element, HMM, Homology, Library Generation | Present (Dec 01 2025) | |
| ISMapper | https://doi.org/10.1186/s12864-015-1860-2 | IS Element, Short Read, NGS/HTS, Illumina, Paired-End, Polymorphism, Genotype | Present (Dec 01 2025) | |
| ISQuest | https://doi.org/10.1093/bioinformatics/btv388 | IS Element, NGS/HTS, Homology | Present (Dec 01 2025) | |
| IScan | https://doi.org/10.1093/nar/gkm597 | IS Element, Homology | Absent (Dec 01 2025) | |
| ISsaga | https://doi.org/10.1186/gb-2011-12-3-r30 | Homology, Annotation, IS Element | Absent (Dec 01 2025) | |
| ISseeker | https://doi.org/10.1099/mgen.0.000062 | IS Element, Homology, Comparative | Present (Dec 01 2025) | |
| ITIS (Identification of Transposon Insertion Sites) | https://doi.org/10.1186/s12859-015-0507-2 | Genotype, Polymorphism, NGS/HTS | Absent (Dec 01 2025) | |
| IUPACpal | https://doi.org/10.1186/s12859-021-03983-2 | Inverted Repeat | Present (Dec 01 2025) | |
| In-seq/Tn-seq | http://doi.org/10.1038/nprot.2011.417 | Tn-Seq, Transposon Mutagenesis | Present (Dec 01 2025) | |
| InFire | https://doi.org/10.1093/bioinformatics/btr672 | Transposon Mutagenesis, Web Server, Restriction Digestion | Absent (Dec 01 2025) | |
| InMut-Finder | https://doi.org/10.1186/s12864-021-08206-9 | NGS/HTS, Oxford Nanopore, Tn-Seq, Transposon Mutagenesis | Present (Dec 01 2025) | |
| Inpactor | https://doi.org/10.3390/biology7020032 | LTR Retrotransposon, Classification, Insertion Time | Present (Dec 01 2025) | |
| Inpactor2 | https://doi.org/10.1093/bib/bbac511 | LTR Retrotransposon, Classification, Insertion Time, Neural Network | Present (Dec 01 2025) | |
| InsertionMapper | https://doi.org/10.1186/1471-2164-14-679 | Tn-Seq, Transposon Mutagenesis, NGS/HTS | Present (Dec 01 2025) | |
| IntegronFinder | https://doi.org/10.1093/nar/gkw319 | Link | Integron, HMM | Present (Dec 01 2025) |
| IntegronFinder 2.0 | https://doi.org/10.3390/microorganisms10040700 | Integron, HMM | Present (Dec 01 2025) | |
| Invade | https://doi.org/10.1093/molbev/msz079 | Simulation, piRNA, Genome | Present (Dec 01 2025) | |
| IpiRId | https://doi.org/10.1371/journal.pone.0179787 | piRNA, SVM | Present (Dec 01 2025) | |
| IslandCafe | https://doi.org/10.1534/g3.119.400562 | Genomic Island | Present (Dec 01 2025) | |
| IslandPath-DIMOB | https://doi.org/10.1093/bioinformatics/bty095 | Genomic Island, HMM, Homology, K-mer | Present (Dec 01 2025) | |
| IslandPick | https://doi.org/10.1186/1471-2105-9-329 | Genomic Island, Homology, Comparative | Absent (Dec 01 2025) | |
| IslandViewer 4 | https://doi.org/10.1093/bioinformatics/btp030 | Genomic Island, Visualization, Web Server | Absent (Dec 01 2025) | |
| JDotter | https://doi.org/10.1093/bioinformatics/btg406 | Dot Plot, Visualization | Present (Dec 01 2025) | |
| Jitterbug | https://doi.org/10.1186/s12864-015-1975-5 | Paired-End, NGS/HTS, Polymorphism, Genotype, | Present (Dec 01 2025) | |
| KKSC Significance Test | https://doi.org/10.1371/journal.pcbi.1004812 | Polymorphism, Genotype, LINE/Non-LTR Retrotransposon, Age, Speciation | Present (Dec 01 2025) | |
| L1EM | https://doi.org/10.1093/bioinformatics/btz724 | Expression, Transcription, LINE1, LINE/Non-LTR Retrotransposon, Activity, NGS/HTS | Present (Dec 01 2025) | |
| L1PD (LINE-1 Pattern Detection) | https://doi.org/10.1186/s12859-022-04907-4 | LINE1, LINE/Non-LTR Retrotransposon, K-mer | Present (Dec 01 2025) | |
| L1Seq | https://doi.org/10.1101/gr.106419.110 | LINE/Non-LTR Retrotransposon, LINE1 | Present (Dec 01 2025) | |
| LAST | https://doi.org/10.1186/s13059-015-0670-9 | Alignment, Repeat | Absent (Dec 01 2025) | |
| LIONS | https://doi.org/10.1093/bioinformatics/btz130 | RNA-Seq, Transcription | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| LTR_FINDER_parallel | https://doi.org/10.1186/s13100-019-0193-0 | LTR Retrotransposon, Structure, HPC | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| LTRclassifier | https://doi.org/10.1080/2159256X.2016.1241050 | Link | LTR Retrotransposon, HMM, Classification, Web Server | Present (Dec 01 2025) |
| LTRdigest | https://doi.org/10.1093/nar/gkp759 | LTR Retrotransposon, Web Server, Structure, Classification | Present (Dec 01 2025) | |
| LTRharvest | https://doi.org/10.1186/1471-2105-9-18 | Link | LTR Retrotransposon, Structure | Present (Dec 01 2025) |
| LTRphyler | https://doi.org/10.1186/1471-2229-13-172 | LTR Retrotransposon, Classification | Absent (Dec 01 2025) | |
| LTRpred | https://doi.org/10.21105/joss.02170 | De Novo, Homology, LTR Retrotransposon, Annotation | Absent (Dec 01 2025) | |
| LTRsift | https://doi.org/10.1186/1759-8753-3-18 | Link | De Novo, LTR Retrotransposon, Visualization, Library Generation, Annotation | Absent (Dec 01 2025) |
| LTRtype | https://doi.org/10.3389/fpls.2017.00402 | LTR Retrotransposon, Nested Insertion, Homology, | Absent (Dec 01 2025) | |
| LoRTE | https://doi.org/10.1186/s13100-017-0088-x | Long Read, PacBio, NGS/HTS, Genotype, Polymorphism, Indel, Homology | Absent (Dec 01 2025) | |
| LoRTIS-SS | https://doi.org/10.1101/2022.05.26.493556 | Long Read, NGS/HTS, Oxford Nanopore, Tn-Seq, Transposon Mutagenesis | Present (Dec 01 2025) | |
| LocaTR | https://doi.org/10.1186/s12864-016-3043-1 | LTR Retrotransposon, Homology, Structure, Annotation | Present (Dec 01 2025) | |
| LocusMasterTE | https://doi.org/10.1101/2023.03.21.533716 | NGS/HTS, Long Read, Expression, Transcription, RNA-Seq | Present (Dec 01 2025) | |
| LongRepMarker | https://doi.org/10.1093/nar/gkab563 | De Novo, K-mer, Library Generation, Long Read, Short Read | Present (Dec 01 2025) | |
| Look4LTRs | https://doi.org/10.1186/s13100-024-00317-w | LTR Retrotransposon, Nested Insertion, Annotation | Present (Dec 01 2025) | |
| LtrDetector | https://doi.org/10.1186/s12864-019-5796-9 | De Novo, LTR Retrotransposon, Structure, Annotation, Visualization | Present (Dec 01 2025) | |
| Lumpy | https://doi.org/10.1186/gb-2014-15-6-r84 | Structural Variation | Present (Dec 01 2025) | |
| MAGenTA | https://doi.org/10.1093/bioinformatics/btx320 | Web Server, Tn-Seq, Transposon Mutagenesis, NGS/HTS, Visualization, Analysis | Present (Dec 01 2025) | |
| MAK (MITE Analysis Kit) | https://doi.org/10.1093/nar/gkg531 | MITE, Homology, Annotation, ITR/TIR/DNA Transposon | Absent (Dec 01 2025) | |
| MANTIS | http://doi.org/10.18632/oncotarget.13918 | Simple Sequence Repeat/Microsatellite, Instability, Cancer, NGS/HTS | Present (Dec 01 2025) | |
| MASiVE | https://doi.org/10.1093/bioinformatics/btq454 | LTR Retrotransposon, Sirevirus, Structure, Repeat Extraction | Absent (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| MCHelper | https://doi.org/10.1101/2023.10.17.562682 | Automated Curation, Classification | Present (Dec 01 2025) | |
| ME-Scan | https://doi.org/10.1186/s13100-020-00207-x | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (Dec 01 2025) | |
| MEGAnE | https://doi.org/10.1101/2022.03.25.485726 | Github | Genotype, Polymorphism, NGS/HTS, Short Read | Present (Dec 01 2025) |
| MELT | https://doi.org/10.1101/gr.218032.116 | Genotype, Polymorphism, Illumina, Paired-End, NGS/HTS | Present (Dec 01 2025) | |
| MGERT | https://doi.org/10.1186/s13100-019-0163-6 | Conserved Domain, Repeat Extraction, De Novo, Library Generation, Repeat Extraction | Present (Dec 01 2025) | |
| MGEScan | https://doi.org/10.1093/bioinformatics/btw157 | Web Server, LTR Retrotransposon, LINE/Non-LTR Retrotransposon, HMM | Present (Dec 01 2025) | |
| MGEfinder | https://doi.org/10.1016/j.chom.2019.10.022 | Archaea, Bacteria, , NGS/HTS, Polymorphism, Library Generation | Present (Dec 01 2025) | |
| MIRU-VNTRplus | https://doi.org/10.1093/nar/gkq351 | Tuberculosis, Genotype, Tandem Repeat, Web Server | Present (Dec 01 2025) | |
| MIRU-profiler | https://doi.org/10.7717/peerj.5090 | Tuberculosis, Genotype, Tandem Repeat | Present (Dec 01 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 (Dec 01 2025) | |
| MITE Digger | https://doi.org/10.1186/1471-2105-14-186 | MITE, Homology, Annotation, ITR/TIR/DNA Transposon | Absent (Dec 01 2025) | |
| MITE Tracker | https://doi.org/10.1186/s12859-018-2376-y | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Present (Dec 01 2025) | |
| MITE-Hunter | https://doi.org/10.1093/nar/gkq862 | MITE, Structure, Annotation, ITR/TIR/DNA Transposon | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| MSGIP | https://doi.org/10.1371/journal.pone.0146352 | Genomic Island, Mean Shift Algorithm | Present (Dec 01 2025) | |
| MSIsensor | https://doi.org/10.1093/bioinformatics/btt755 | Simple Sequence Repeat/Microsatellite, Instability, Polymorphism, Genotype, NGS/HTS, Cancer | Present (Dec 01 2025) | |
| MTGIpick | https://doi.org/10.1093/bib/bbw118 | Genomic Island, K-mer | Present (Dec 01 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 (Dec 01 2025) | |
| MacSyFinder | https://doi.org/10.1371/journal.pone.0110726 | CRISPR, HMM | Present (Dec 01 2025) | |
| McClintock | https://doi.org/10.1534/g3.117.043893 | Genotype, Polymorphism, NGS/HTS | Present (Dec 01 2025) | |
| McClintock2 | https://doi.org/10.1101/2023.02.13.528343 | Genotype, Polymorphism, NGS/HTS | Present (Dec 01 2025) | |
| MegaLTR | https://doi.org/10.3389/fpls.2023.1237426 | Webserver | LTR Retrotransposon, Detection, Annotation, Web Server, Pipeline | Present (Dec 01 2025) |
| MetaCompare | https://doi.org/10.1093/femsec/fiy079 | NGS/HTS, Metagenomics, AMR/Antibiotic Resistance, BLAST, Pathogen | Present (Dec 01 2025) | |
| MetaPhage | https://doi.org/10.1101/2022.04.17.488583 | NGS/HTS, Metagenomics, Annotation, Classification, Prophage/Bacteriophage | Present (Dec 01 2025) | |
| MiMSI | https://doi.org/10.1101/2020.09.16.299925 | Simple Sequence Repeat/Microsatellite, Cancer | Present (Dec 01 2025) | |
| MindTheGap | https://doi.org/10.1093/bioinformatics/btu545 | NGS/HTS, Polymorphism, Genotype, K-mer | Present (Dec 01 2025) | |
| MiteFinder | https://doi.org/10.1109/BIBM.2017.8217644 | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Present (Dec 01 2025) | |
| MiteFinderII | https://doi.org/10.1186/s12920-018-0418-y | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Present (Dec 01 2025) | |
| MobileElementFinder | https://doi.org/10.1093/jac/dkaa390 | IS Element, AMR/Antibiotic Resistance, Plasmid, Homology, Web Server | Absent (Dec 01 2025) | |
| MobilomeFINDER | https://doi.org/10.1093/nar/gkm380 | Genomic Island, Microarray, Web Server | Absent (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| NCRF | https://doi.org/10.1093/bioinformatics/btz484 | Long Read, NGS/HTS, Tandem Repeat, De Novo | Present (Dec 01 2025) | |
| NGSEP | https://doi.org/10.1002/aps3.11520 | https://sourceforge.net/projects/ngsep/ | Repeat Masking, Annotation | Present (Dec 01 2025) |
| NGSEP (Next-Generation Sequencing Experience Platform) | https://doi.org/10.1002/aps3.11520 | Github | NGS/HTS, Homology, Long Read, Annotation | Present (Dec 01 2025) |
| 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 (Dec 01 2025) | |
| NanoSatellite | https://doi.org/10.1186/s13059-019-1856-3 | NGS/HTS, Oxford Nanopore, Tandem Repeat | Present (Dec 01 2025) | |
| NanoTRF | https://doi.org/10.3390/plants11162103 | NGS/HTS, Oxford Nanopore, Tandem Repeat | Present (Dec 01 2025) | |
| NanoVar | https://doi.org/10.1186/s13059-020-01968-7 | NGS/HTS, Oxford Nanopore, Polymorphism, Genotype | Present (Dec 01 2025) | |
| NanoWgsTE | https://doi.org/10.1101/2021.06.11.448052 | Oxford Nanopore, CRISPR, Eukaryotic Transposon | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| OASIS | https://doi.org/10.1101/2020.11.02.365809 | IS Element, Homology, Classification | Present (Dec 01 2025) | |
| OMWSA (Optimized Moving Window Spectral Analysis) | https://doi.org/10.1093/bioinformatics/btm008 | Visualization, Repeat | Absent (Dec 01 2025) | |
| OSTRFPD | https://doi.org/10.1177%2F1176934319843130 | Simple Sequence Repeat/Microsatellite, Alignment, Repeat Extraction, Annotation | Present (Dec 01 2025) | |
| One_code_to_find_them_all | https://doi.org/10.1186/1759-8753-5-13 | Repeat Extraction, Abundance | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| 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 (Dec 01 2025) |
| PATIMDB | https://doi.org/10.1002/0471142727.mb1907s86 | Tn-Seq, Transposon Mutagenesis | Absent (Dec 01 2025) | |
| PAtChER | https://doi.org/10.1101/2021.08.25.457666 | ChIP-Seq | Present (Dec 01 2025) | |
| PHACTS | https://doi.org/10.1093/bioinformatics/bts014 | Prophage/Bacteriophage, Classification | Present (Dec 01 2025) | |
| PHAST | https://doi.org/10.1093/nar/gkr485 | Prophage/Bacteriophage, Web Server, Homology, Annotation, Visualization | Absent (Dec 01 2025) | |
| PHASTER | https://doi.org/10.1093/nar/gkw387 | Prophage/Bacteriophage, Web Server, Homology, Annotation, Visualization | Present (Dec 01 2025) | |
| PIATEA | HMM, Annotation Track | Present (Dec 01 2025) | ||
| PILER | https://doi.org/10.1093/bioinformatics/bti1003 | De Novo, Library Generation | Present (Dec 01 2025) | |
| PILFER | https://doi.org/10.1016/j.ygeno.2017.12.005 | piRNA, RNA-Seq, NGS/HTS | Present (Dec 01 2025) | |
| PIMMS (Pragmatic Insertional Mutation Mapping System) | https://doi.org/10.3389/fgene.2015.00139 | NGS/HTS, Tn-Seq | Present (Dec 01 2025) | |
| PIMMS-Dash | https://doi.org/10.1016/j.csbj.2024.10.025 | Link | Web Server, Transposon Mutagenesis, Tn-Seq | Present (Dec 01 2025) |
| PIPS | https://doi.org/10.1371/journal.pone.0030848 | Genomic Island, Pathogenicity Island, Prediction | Absent (Dec 01 2025) | |
| PPR-Meta | https://doi.org/10.1093/gigascience/giz066 | Link | Prophage/Bacteriophage, Plasmid, Deep Learning | Absent (Dec 01 2025) |
| PRAP | https://doi.org/10.1093/bioinformatics/btt482 | De Novo, Library Generation, Repeat Masking, Archaea, Bacteria | Present (Dec 01 2025) | |
| PSSV | https://doi.org/10.1093/bioinformatics/btw605 | Structural Variation, NGS/HTS | Absent (Dec 01 2025) | |
| PTEMD | https://doi.org/10.1093/dnares/dsw011 | Short Read, NGS/HTS, Genotype, Polymorphism, De Novo | Absent (Dec 01 2025) | |
| PacmonSTR | https://doi.org/10.1093/bioinformatics/btu437 | Tandem Repeat, NGS/HTS, Long Read, HMM, Homology | Present (Dec 01 2025) | |
| PaliDIS | https://doi.org/10.1099/mgen.0.000917 | IS Element, Metagenomics, Annotation | Present (Dec 01 2025) | |
| [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 (Dec 01 2025) | |
| ParasiTE | https://doi.org/10.1101/2022.09.21.507229 | Long Read, NGS/HTS, RNA-Seq, Expression, Transcription | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| PhaGenus | https://doi.org/10.1093/bib/bbad408 | Prophage/Bacteriophage, Classification | Present (Dec 01 2025) | |
| Phage Commander | https://doi.org/10.1101/2020.11.11.378802 | Prophage/Bacteriophage, Pipeline | Present (Dec 01 2025) | |
| PhageAI | https://doi.org/10.1101/2020.07.11.198606 | Prophage/Bacteriophage, Web Server, Machine Learning, Classification | Present (Dec 01 2025) | |
| PhageWeb | https://doi.org/10.3389/fgene.2018.00644 | Prophage/Bacteriophage, Web Server, GC, tRNA | Absent (Dec 01 2025) | |
| Phage_Finder | https://doi.org/10.1093/nar/gkl732 | Prophage/Bacteriophage, Homology, HMM | Present (Dec 01 2025) | |
| PhiSpy | https://doi.org/10.1093/nar/gks406 | Prophage/Bacteriophage, Homology | Present (Dec 01 2025) | |
| Phigaro | https://doi.org/10.1093/bioinformatics/btaa250 | Prophage/Bacteriophage, Annotation | Present (Dec 01 2025) | |
| Phobos | Simple Sequence Repeat/Microsatellite, Library Generation | Present (Dec 01 2025) | ||
| PhyLTR | LTR Retrotransposon, Annotation, Pipeline, Gene Conversion, Classification, Phylogeny | Present (Dec 01 2025) | ||
| PiRATE | https://doi.org/10.1186/s12864-018-4763-1 | Web Server, Homology, HMM, Structure, De Novo, Classification, Library Generation, Annotation | Present (Dec 01 2025) | |
| Piano | https://doi.org/10.1186/s12859-014-0419-6 | piRNA, SVM, Classification, Web Server | Absent (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| PingPongPro | https://doi.org/10.1093/bioinformatics/bty578 | piRNA, RNA-Seq, NGS/HTS | Present (Dec 01 2025) | |
| PlasForest | https://doi.org/10.1186/s12859-021-04270-w | Plasmid, Homology, Classification | Present (Dec 01 2025) | |
| PlasLR | https://doi.org/10.1101/2021.06.14.448306 | Plasmid, Long Read | Present (Dec 01 2025) | |
| PlasTrans | https://doi.org/10.1099/mgen.0.000459 | Plasmid | Present (Dec 01 2025) | |
| Plasflow | https://doi.org/10.1093/nar/gkx1321 | Plasmid, Metagenomics, Neural Network | Present (Dec 01 2025) | |
| PlasmidFinder | https://doi.org/10.1128/aac.02412-14 | Plasmid, Homology | Absent (Dec 01 2025) | |
| PlasmidHunter | https://doi.org/10.1101/2023.02.01.526640 | Link | Plasmid, Web Server | Present (Dec 01 2025) |
| PlasmidTron | https://doi.org/10.1099/mgen.0.000164 | Plasmid, K-mer | Present (Dec 01 2025) | |
| PlotRep | https://doi.org/10.1093/nar/gkl263 | Dot Plot, Visualization, Repeat Merging | Absent (Dec 01 2025) | |
| PoPoolationTE | https://doi.org/10.1093/molbev/msw137 | Genotype, Polymorphism, NGS/HTS | Present (Dec 01 2025) | |
| PolyMorphPredict | https://doi.org/10.3389/fpls.2018.01966 | Simple Sequence Repeat/Microsatellite, Primer, Web Server | Absent (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| ProGeRF | http://doi.org/10.1155/2015/394157 | Simple Sequence Repeat/Microsatellite, Annotation | Absent (Dec 01 2025) | |
| Process_hits | https://doi.org/10.1186/1756-0500-4-482 | Repeat Extraction, Alignment | Present (Dec 01 2025) | |
| ProphET | https://doi.org/10.1371/journal.pone.0223364 | Prophage/Bacteriophage, Homology, Annotation | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| Pysim-sv | https://doi.org/10.1186/s12859-017-1464-8 | Structural Variation, NGS/HTS, Simulation | Present (Dec 01 2025) | |
| QDD | https://doi.org/10.1093/bioinformatics/btp670 | Simple Sequence Repeat/Microsatellite, Primer | Absent (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| RAREFAN (RAyt/REpin Finder and ANalyzer) | https://doi.org/10.24072/pcjournal.244 | Web Server, REPIN/RAYT, Annotation | Absent (Dec 01 2025) | |
| RBR | https://doi.org/10.1093/bioinformatics/btl368 | Expression, Transcription, RNA-Seq, Repeat Masking, De Novo | Absent (Dec 01 2025) | |
| REPCLASS | https://uta-ir.tdl.org/uta-ir/handle/10106/455 | Classification | Present (Dec 01 2025) | |
| REPET | https://doi.org/10.1371/journal.pone.0016526 | Link | De Novo, Homology, Structure, Library Generation, Annotation | Present (Dec 01 2025) |
| REPdenovo | https://doi.org/10.1371/journal.pone.0150719 | Short Read, NGS/HTS, De Novo, Assembly | Present (Dec 01 2025) | |
| REPuter | https://doi.org/10.1093/nar/29.22.4633 | Repeat, Library Generation, De Novo | Present (Dec 01 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 (Dec 01 2025) |
| REannotate | https://doi.org/10.1186/1471-2164-9-614 | Annotation Parsing, Nested Insertion | Present (Dec 01 2025) | |
| REdiscoverTE | https://doi.org/10.1038/s41467-019-13035-2 | Expression, Transcription, RNA-Seq | Present (Dec 01 2025) | |
| RFPlasmid | https://doi.org/10.1101/2020.07.31.230631 | Link | Plasmid, Resistance, AMR/Antibiotic Resistance, K-mer, Homology | Present (Dec 01 2025) |
| RIPCAL | https://doi.org/10.1186/1471-2105-9-478 | RIP/Repeat-Induced Point Mutation, Mutation, Alignment, Repeat | Present (Dec 01 2025) | |
| RISCI (Repeat Induced Sequence Changes Identifier) | https://doi.org/10.1186/1471-2105-11-609 | NGS/HTS, Genotype, Polymorphism | Absent (Dec 01 2025) | |
| RJPrimers | https://doi.org/10.1093/nar/gkq425 | Homology, Primer | Absent (Dec 01 2025) | |
| RNA2DSearch | https://doi.org/10.1261/rna.1264109 | RNA Localization, Prediction, Web Server | Absent (Dec 01 2025) | |
| RPT (Repeat Pattern Toolkit) | Repeat Annotation | |||
| RSPB | https://doi.org/10.1093/molbev/msr282 | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Absent (Dec 01 2025) | |
| RSVSim | https://doi.org/10.1093/bioinformatics/btt198 | Structural Variation, Simulation | Present (Dec 01 2025) | |
| RTAnalyzer | https://doi.org/10.1093/nar/gkm313 | LINE1, LINE/Non-LTR Retrotransposon, Homology | Absent (Dec 01 2025) | |
| RTclass1 | https://doi.org/10.1016/j.gene.2009.07.019 | Classification, LINE/Non-LTR Retrotransposon | Absent (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| RepAHR | https://doi.org/10.1186/s12859-020-03779-w | De Novo, Library Generation, NGS/HTS, K-mer | Present (Dec 01 2025) | |
| RepARK | https://doi.org/10.1093/nar/gku210 | De Novo, Library Generation, NGS/HTS | Present (Dec 01 2025) | |
| RepBox | https://doi.org/10.1186/s12859-023-05419-5 | TE Detection, TE Annotation, Plants | Present (Dec 01 2025) | |
| RepBox | https://doi.org/10.1186/s12859-023-05419-5 | Detection, Annotation, Classification, Pipeline | Present (Dec 01 2025) | |
| RepEnrich | https://doi.org/10.1186/1471-2164-15-583 | NGS/HTS, RNA-Seq, Expression | Present (Dec 01 2025) | |
| RepEnrich2 | NGS/HTS, RNA-Seq, Expression | Present (Dec 01 2025) | ||
| RepExpress | https://doi.org/10.1002/cpz1.206 | Pipeline, RNA-Seq, Expression | Present (Dec 01 2025) | |
| RepLoc | https://doi.org/10.1093/bib/bbaa086 | Repeat, K-mer, Visualization, Annotation, Web Server | Absent (Dec 01 2025) | |
| RepLong | https://doi.org/10.1093/bioinformatics/btx717 | De Novo, Long Read, NGS/HTS | Present (Dec 01 2025) | |
| RepMiner | https://doi.org/10.1101/gr.083360.108 | Repeat, Library Generation, De Novo | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| Repeat Expansion Viewer (REViewer) | Short Read, NGS/HTS, Short Tandem Repeat | Present (Dec 01 2025) | ||
| RepeatAnalyzer | https://doi.org/10.1186/s12864-016-2686-2 | Simple Sequence Repeat/Microsatellite, Summary, Genotype | Present (Dec 01 2025) | |
| RepeatCraft | https://doi.org/10.1093/bioinformatics/bty745 | Nested Insertion, Visualization | Present (Dec 01 2025) | |
| RepeatExplorer | https://doi.org/10.1093/bioinformatics/btt054 | Link | De Novo, Library Generation, Annotation, NGS/HTS | Present (Dec 01 2025) |
| RepeatFiller | https://doi.org/10.1093/gigascience/giz132 | Genome Alignment, Repeat | Present (Dec 01 2025) | |
| RepeatFinder | https://doi.org/10.1186/gb-2001-2-8-research0027 | Library Generation | Present (Dec 01 2025) | |
| RepeatGluer | https://doi.org/10.1101/gr.2395204 | Repeat Annotation | ||
| RepeatMasker | Repeat Masking, Annotation | Present (Dec 01 2025) | ||
| RepeatModeler | https://doi.org/10.1073/pnas.1921046117 | GitHub | De Novo, Library Generation, Structure, Seed Alignment, Classification | Absent (Dec 01 2025) |
| RepeatProfiler | https://doi.org/10.1101/2020.05.22.111252 | NGS/HTS, Short Read, Visualization, Repeat | Present (Dec 01 2025) | |
| RepeatRunner | https://doi.org/10.1016/j.gene.2006.09.011 | De Novo, Library Generation | Present (Dec 01 2025) | |
| RepeatScout | https://doi.org/10.1093/bioinformatics/bti1018 | De Novo, Library Generation | Present (Dec 01 2025) | |
| RepeatSeq | https://doi.org/10.1093/nar/gks981 | Simple Sequence Repeat/Microsatellite, Genotype, Polymorphism, NGS/HTS | Present (Dec 01 2025) | |
| Repguide | CRISPR, gRNA, Repeat | Present (Dec 01 2025) | ||
| Repsc | Expression, RNA-Seq, Single-Cell | Present (Dec 01 2025) | ||
| Repseek | https://doi.org/10.1093/bioinformatics/btl519 | Repeat, Library Generation, De Novo | Absent (Dec 01 2025) | |
| RetroMap | https://doi.org/10.1186/gb-2004-5-10-r78 | LTR Retrotransposon, Visualization | Absent (Dec 01 2025) | |
| RetroSnake | https://doi.org/10.1101/2022.04.08.487607 | NGS/HTS, ERV/Endogenous Retrovirus, Annotation | Present (Dec 01 2025) | |
| RetroSom | https://doi.org/10.1101/660779 | Machine Learning, NGS/HTS, Genotype, Polymorphism | Present (Dec 01 2025) | |
| RetroTector | https://doi.org/10.1093/nar/gkm515 | ERV/Endogenous Retrovirus | Present (Dec 01 2025) | |
| Retroseq | https://doi.org/10.1093/bioinformatics/bts697 | Genotype, Polymorphism, NGS/HTS, Illumina, Paired-End | Present (Dec 01 2025) | |
| SAT | https://doi.org/10.1186/1471-2105-8-465 | Simple Sequence Repeat/Microsatellite, Primer, Library Generation, Web Server | Absent (Dec 01 2025) | |
| SATEComp | Link | Homology, Keyword Search, Web Server | Absent (Dec 01 2025) | |
| SCNVSim | https://doi.org/10.1186/s12859-015-0502-7 | CNV/Copy Number Variation, Simulation, Structural Variation | Present (Dec 01 2025) | |
| SCRAMble | https://doi.org/10.1038/s41436-020-0749-x | NGS/HTS, Genotype, Polymorphism, Paired-End | Present (Dec 01 2025) | |
| SECNVs | https://doi.org/10.3389/fgene.2020.00082 | CNV/Copy Number Variation, Simulation, Expression | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| SIGAR | https://doi.org/10.1101/2020.05.05.079426 | NGS/HTS, Short Read, Split Read | Present (Dec 01 2025) | |
| SIGI-HMM | https://doi.org/10.1186/1471-2105-7-142 | Genomic Island, Codon Usage, HMM | Absent (Dec 01 2025) | |
| SINE-Finder | https://doi.org/10.1105/tpc.111.088682 | SINE, Homology, Motif, Library Generation | Absent (Dec 01 2025) | |
| SINE_Scan | https://doi.org/10.1093/bioinformatics/btw718 | SINE, Library Generation, Annotation | Present (Dec 01 2025) | |
| SINEsFIND | https://doi.org/10.1093/dnares/dsw048 | SINE, Expression, RNA-Seq, NGS/HTS | Present (Dec 01 2025) | |
| SMaRTFinder | Repeat, Annotation | Absent (Dec 01 2025) | ||
| SPLITREADER | https://doi.org/10.7554/eLife.15716.001 | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (Dec 01 2025) | |
| SQUID | https://doi.org/10.1186/s13059-018-1421-5 | RNA-Seq, Expression, NGS/HTS, Structural Variation, Fusion | Present (Dec 01 2025) | |
| SQuIRE | https://doi.org/10.1093/nar/gky1301 | NGS/HTS, RNA-Seq, Expression | Present (Dec 01 2025) | |
| SRC (Spark-based RepeatClassifier) | https://doi.org/10.1101/2021.06.03.446998 | RepeatMasker, Classification | Present (Dec 01 2025) | |
| SRF | https://doi.org/10.1093/bioinformatics/bth103 | Repeat, Web Server | Absent (Dec 01 2025) | |
| SRF (Satellite Repeat Finder) | https://doi.org/10.1101/gr.278005.123 | Simple Sequence Repeat/Microsatellite, NGS/HTS, Library Generation | Present (Dec 01 2025) | |
| SSR Locator | http://dx.doi.org/10.1155/2008/412696 | Simple Sequence Repeat/Microsatellite, Primer, PCR, Library Generation | Absent (Dec 01 2025) | |
| SSR Primer | https://doi.org/10.1093/bioinformatics/bth104 | Simple Sequence Repeat/Microsatellite, Primer, Library Generation | Absent (Dec 01 2025) | |
| SSRIT | Simple Sequence Repeat/Microsatellite, Summary | Absent (Dec 01 2025) | ||
| 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 (Dec 01 2025) | |
| STEAK | https://doi.org/10.1093/ve/vex023 | NGS/HTS, Genotype, Polymorphism, Annotation | Present (Dec 01 2025) | |
| STRipy | https://doi.org/10.1101/2021.06.13.448220 | Link | Short Tandem Repeat, Genotype, NGS/HTS | Present (Dec 01 2025) |
| STRling | https://doi.org/10.1186/s13059-022-02826-4 | Short Tandem Repeat, Annotation, NGS/HTS | Present (Dec 01 2025) | |
| SURVIVOR | https://doi.org/10.1038/ncomms14061 | Structural Variation, NGS/HTS, Simulation | Present (Dec 01 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 (Dec 01 2025) | |
| SV2 | https://doi.org/10.1093/bioinformatics/btx813 | Structural Variation, Machine Learning, Paired-End | Present (Dec 01 2025) | |
| SVDSS | https://doi.org/10.1038/s41592-022-01674-1 | NGS/HTS, Structural Variation, Long Read | Present (Dec 01 2025) | |
| SVDetect | https://doi.org/10.1093/bioinformatics/btq293 | NGS/HTS, Structural Variation, Paired-End | Present (Dec 01 2025) | |
| SVEngine | https://doi.org/10.1093/gigascience/giy081 | Structural Variation, Simulation | Present (Dec 01 2025) | |
| SVIM | https://doi.org/10.1093/bioinformatics/btz041 | NGS/HTS, Long Read, Structural Variation | Present (Dec 01 2025) | |
| SVM2 | https://doi.org/10.1093/nar/gks606 | Structural Variation, Supervised Learning | ||
| SVPV | https://doi.org/10.1093/bioinformatics/btx117 | Structural Variation, Visualization | Present (Dec 01 2025) | |
| SVXplorer | https://doi.org/10.1371/journal.pcbi.1007737 | NGS/HTS, Paired-End, Structural Variation | Present (Dec 01 2025) | |
| SVelter | https://doi.org/10.1186/s13059-016-0993-1 | Structural Variation, NGS/HTS | Present (Dec 01 2025) | |
| SVmine | https://doi.org/10.1093/bioinformatics/btx455 | Structural Variation, Pipeline | Present (Dec 01 2025) | |
| SWGIS v2.0 | https://doi.org/10.1186/s12864-018-4724-8 | Genomic Island, Eukaryote, K-mer | Present (Dec 01 2025) | |
| SalmonTE | https://doi.org/10.1142/9789813235533_0016 | RNA-Seq, Expression, NGS/HTS, Homology | Present (Dec 01 2025) | |
| SatDNA Analyzer | https://doi.org/10.1093/bioinformatics/btm005 | Simple Sequence Repeat/Microsatellite, Alignment, Library Generation | Present (Dec 01 2025) | |
| SciRoKo | https://doi.org/10.1093/bioinformatics/btm157 | Simple Sequence Repeat/Microsatellite, Summary, Annotation | Present (Dec 01 2025) | |
| Signature.py | https://doi.org/10.1007/978-1-4939-0931-5_12 | Small RNA, piRNA, NGS/HTS | Present (Dec 01 2025) | |
| SimulaTE | https://doi.org/10.1093/bioinformatics/btx772 | Simulation, Genome, NGS/HTS, Genotype, Polymorphism | Present (Dec 01 2025) | |
| SoftSV | https://doi.org/10.1093/bib/bbv028 | Structural Variation, Paired-End | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| Sputnik | https://doi.org/10.1038/ng822 | Simple Sequence Repeat/Microsatellite | Absent (Dec 01 2025) | |
| StainedGlass | https://doi.org/10.1093/bioinformatics/btac018 | Link | Simple Sequence Repeat/Microsatellite, Tandem Repeat, Visualization | Present (Dec 01 2025) |
| SyRI | https://doi.org/10.1186/s13059-019-1911-0 | Structural Variation, NGS/HTS, Comparative, Whole Genome | Present (Dec 01 2025) | |
| T-REKS | https://doi.org/10.1093/bioinformatics/btp482 | Tandem Repeat | Absent (Dec 01 2025) | |
| T-lex | https://doi.org/10.1093/nar/gkq1291 | Genotype, Polymorphism, NGS/HTS | Absent (Dec 01 2025) | |
| T-lex2 | https://doi.org/10.1093/nar/gku1250 | Genotype, Polymorphism, NGS/HTS | Present (Dec 01 2025) | |
| T-lex3 | https://doi.org/10.1093/bioinformatics/btz727 | Genotype, Polymorphism, NGS/HTS | Present (Dec 01 2025) | |
| T3E | https://doi.org/10.1186/s13100-022-00285-z | ChIP-Seq, NGS/HTS | Present (Dec 01 2025) | |
| TANGRAM | https://doi.org/10.1186/1471-2164-15-795 | Polymorphism, Genotype, NGS/HTS | Present (Dec 01 2025) | |
| TAPDANCE | https://doi.org/10.1186/1471-2105-13-154 | Genotype, Polymorphism, NGS/HTS | Present (Dec 01 2025) | |
| TAPO | https://doi.org/10.1016/j.febslet.2015.08.025 | Tandem Repeat, Web Server | Absent (Dec 01 2025) | |
| TARDIS | http://dx.doi.org/10.1016/j.ymeth.2017.05.030 | Structural Variation, NGS/HTS | Present (Dec 01 2025) | |
| TARGeT (Tree Analysis of Related Genes and Transposons) | https://doi.org/10.1093/nar/gkp295 | Homology, Web Server | Present (Dec 01 2025) | |
| TASR | https://doi.org/10.1093/nar/gkv257 | Small RNA, Annotation | Present (Dec 01 2025) | |
| TCF | https://doi.org/10.1371/journal.pcbi.0030137 | Nested Insertion, Annotation, Web Server | Absent (Dec 01 2025) | |
| TE (Insertion/Deletion Dynamics for Transposable Elements) | https://doi.org/10.1534/genetics.118.301198 | Indel, Insertion Time, LTR Retrotransposon, Aegilops | Present (Dec 01 2025) | |
| TE Displayer | https://doi.org/10.1093/bioinformatics/btq639 | TE Display | Absent (Dec 01 2025) | |
| TE transcripts | https://doi.org/10.1093/bioinformatics/btv422 | Expression, Transcription, RNA-Seq | Present (Dec 01 2025) | |
| TE-Aid | https://doi.org/10.1186/s13100-021-00259-7 | Annotation, Classification, Manual Curation, TE Libraries QC | Present (Dec 01 2025) | |
| TE-Learner | https://doi.org/10.1371/journal.pcbi.1006097 | Machine Learning, LTR Retrotransposon, Classification | Absent (Dec 01 2025) | |
| TE-Seq | https://doi.org/10.1101/2024.10.11.617912 | Annotation, RNA-Seq, Transcription, Expression | Present (Dec 01 2025) | |
| TE-Tracker | https://doi.org/10.1186/s12859-014-0377-z | Polymorphism, Genotype | Present (Dec 01 2025) | |
| TE-greedy-nester | https://doi.org/10.1093/bioinformatics/btaa632 | Link | Nested Insertion, LTR Retrotransposon | Present (Dec 01 2025) |
| TE-invasion-simulations | https://doi.org/10.1093/gbe/evy218 | Simulation, Genome, Evolution | Present (Dec 01 2025) | |
| TE-locate | https://doi.org/10.3390/biology1020395 | NGS/HTS, Paired-End, Genotype, Polymorphism | Present (Dec 01 2025) | |
| TE-nester | https://ieeexplore.ieee.org/document/8621071 | Structure, Nested Insertion | Present (Dec 01 2025) | |
| TE-reX | https://doi.org/10.1101/2020.07.02.163816 | Genotype, Polymorphism, Recombination | Present (Dec 01 2025) | |
| TEA | https://doi.org/10.1126/science.1222077 | Genotype, Polymorphism | Present (Dec 01 2025) | |
| TEBreak | https://doi.org/10.1186/s13100-016-0076-6 | Genotype, Polymorphism, NGS/HTS | Present (Dec 01 2025) | |
| TECDetec | https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.718854 | Expression, Transcription, Chimera, NGS/HTS | Present (Dec 01 2025) | |
| TECookbook | https://doi.org/10.1093/nargab/lqad078 | ChIP-Seq, NGS/HTS, Analysis | Present (Dec 01 2025) | |
| TEF (Transposable Element Finder) | https://doi.org/10.1186/s12859-022-05011-3 | Polymorphism, Genotype, NGS/HTS | Present (Dec 01 2025) | |
| TEFLoN | https://doi.org/10.1093/gbe/evx050 | Annotation, Classification, NGS/HTS, Polymorphism, Genotype, Paired-End, Illumina | Present (Dec 01 2025) | |
| TEGRiP | https://doi.org/10.1101/2021.02.25.432867 | Eukaryotic Transposon, Annotation, Gene | Present (Dec 01 2025) | |
| TELR | NGS/HTS, PacBio, Oxford Nanopore, Long Read, Genotype, Polymorphism | Present (Dec 01 2025) | ||
| TEMP | https://doi.org/10.1093/nar/gku323 | Genotype, Polymorphism, NGS/HTS | Present (Dec 01 2025) | |
| TEMP2 | https://doi.org/10.1093/nar/gkab010 | Genotype, Polymorphism, NGS/HTS, Short Read | Present (Dec 01 2025) | |
| TEPEAK | https://doi.org/10.1101/2023.10.13.562297 | Genotype, Polymorphism, NGS/HTS | Present (Dec 01 2025) | |
| TEPID | https://doi.org/10.7554/eLife.20777.001 | Polymorphism, Genotype, NGS/HTS | Present (Dec 01 2025) | |
| TERAD | https://doi.org/10.1111/1755-0998.13080 | RAD-Seq, Repeat Masking, Annotation | Present (Dec 01 2025) | |
| TERL | https://doi.org/10.1093/bib/bbaa185 | Classification, Neural Network | Present (Dec 01 2025) | |
| TESD | https://doi.org/10.1093/bioinformatics/btl454 | Simulation, Genome | Absent (Dec 01 2025) | |
| TESeeker | https://doi.org/10.1186/1471-2105-12-130 | Homology, VirtualBox, Library Generation | Absent (Dec 01 2025) | |
| TETyper | https://doi.org/10.1099/mgen.0.000232 | Short Read, Paired-End, Polymorphism, Genotype, Archaea, Bacteria | Present (Dec 01 2025) | |
| TE_Density | https://doi.org/10.1186/s13100-022-00264-4 | Annotation, Analysis | Present (Dec 01 2025) | |
| TE_Discovery | https://doi.org/10.1101/701888 | Homology, Library Generation, Annotation, Analysis | Present (Dec 01 2025) | |
| TEcandidates | https://doi.org/10.1093/bioinformatics/bty423 | Expression, Transcription, RNA-Seq | Present (Dec 01 2025) | |
| TEclass | https://doi.org/10.1093/bioinformatics/btp084 | Classification | Present (Dec 01 2025) | |
| TEclass2 | https://doi.org/10.1101/2023.10.13.562246 | Classification, Web Server | Present (Dec 01 2025) | |
| TEffectR | https://doi.org/10.7717/peerj.8192 | RNA-Seq, Expression, NGS/HTS, Homology, Annotation | Present (Dec 01 2025) | |
| TEfinder | https://doi.org/10.3390/genes12020224 | Polymorphism, Genotype, NGS/HTS | Present (Dec 01 2025) | |
| TElocal | Expression, Transcription, RNA-Seq | Present (Dec 01 2025) | ||
| TEmarker | https://doi.org/10.1016/j.xplc.2021.100270 | Genotype, Polymorphism, NGS/HTS | Present (Dec 01 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 (Dec 01 2025) | |
| TEpeaks | ChIP-Seq | Present (Dec 01 2025) | ||
| TEsmall | https://doi.org/10.3389/fgene.2018.00461 | NGS/HTS, Small RNA, piRNA, Annotation | Present (Dec 01 2025) | |
| TEsorter | https://doi.org/10.1093/hr/uhac017 | Link | Classification, HMM | Present (Dec 01 2025) |
| TEspeX | https://doi.org/10.1093/bioinformatics/btac526 | Zenodo | NGS/HTS, Abundance, Expression, Transcription | Present (Dec 01 2025) |
| TIDAL | https://doi.org/10.1093/nar/gkv1193 | Genotype, Polymorphism, Illumina, Drosophila | Present (Dec 01 2025) | |
| TIDDIT | https://f1000research.com/articles/6-664/v2 | Rearrangement, NGS/HTS, Structural Variation | Present (Dec 01 2025) | |
| TIDK (Telomere Identifcation toolKit) | Github | De Novo, Telomere, Visualization | Present (Dec 01 2025) | |
| TIF (Transposon Insertion Finder) | https://doi.org/10.1186/1471-2105-15-71 | NGS/HTS, Genotype, Polymorphism, Short Read | Present (Dec 01 2025) | |
| TIGER (Target Integrative Genetic Element Retriever) | https://doi.org/10.1093/nar/gkaa156 | ICE/Integrative and Conjugative Element, Prophage/Bacteriophage | Present (Dec 01 2025) | |
| TIP_finder | https://doi.org/10.3390/biology9090281 | NGS/HTS, Genotype, Polymorphism | Present (Dec 01 2025) | |
| TIPseq-Hunter | https://doi.org/10.1073/pnas.1619797114 | Paired-End, Illumina, Machine Learning | Present (Dec 01 2025) | |
| TIR-Finder | https://doi.org/10.4137/EBO.S10619 | ITR/TIR/DNA Transposon, Web Server, Homology, Structure | Present (Dec 01 2025) | |
| TIR-Learner | https://doi.org/10.1016/j.molp.2019.02.008 | ITR/TIR/DNA Transposon, Homology, Structure, Annotation | Present (Dec 01 2025) | |
| TIRMITE | MITE, HMM, ITR/TIR/DNA Transposon, Annotation | Present (Dec 01 2025) | ||
| 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 (Dec 01 2025) | |
| TRANSIT | https://doi.org/10.1371/journal.pcbi.1004401 | Tn-Seq, Transposon Mutagenesis | Present (Dec 01 2025) | |
| TRANSPO | ITR/TIR/DNA Transposon, Homology | Absent (Dec 01 2025) | ||
| TRANScendence | https://doi.org/10.1186/s12859-017-1824-4 | De Novo, Homology, Structure, Library Generation, Annotation, Web Server | Present (Dec 01 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 (Dec 01 2025) | |
| TRF | https://doi.org/10.1093/nar/27.2.573 | Tandem Repeat | Present (Dec 01 2025) | |
| TRGT (Tandem Repeat Genotyping Tool) | https://doi.org/10.1101/2023.05.12.540470 | Tandem Repeat, PacBio, Long Read, NGS/HTS, Genotype | Present (Dec 01 2025) | |
| TROLL | https://doi.org/10.1093/bioinformatics/18.4.634 | Tandem Repeat | Present (Dec 01 2025) | |
| TRTools | https://doi.org/10.1101/2020.03.17.996033 | Tandem Repeat, Genotype | Present (Dec 01 2025) | |
| TRcaller | https://doi.org/10.1101/2023.02.15.528687 | Tandem Repeat, NGS/HTS, Long Read, Short Read | Absent (Dec 01 2025) | |
| TRiCoLOR | https://doi.org/10.1093/gigascience/giaa101 | Tandem Repeat, NGS/HTS, Long Read | Present (Dec 01 2025) | |
| TSDFinder | https://doi.org/10.1186/gb-2002-3-10-research0052 | LINE1, LINE/Non-LTR Retrotransposon, Target Site Duplication | Absent (Dec 01 2025) | |
| Tallymer | https://doi.org/10.1186/1471-2164-9-517 | K-mer Counting | Present (Dec 01 2025) | |
| Tandem Repeat Annotation Library | https://doi.org/10.1093/bioinformatics/btv306 | Tandem Repeat, Annotation | Absent (Dec 01 2025) | |
| TandemTools | https://doi.org/10.1093/bioinformatics/btaa440 | Tandem Repeat, Long Read, NGS/HTS, Assembly Polishing, Read Mapping | Present (Dec 01 2025) | |
| TeXP | https://doi.org/10.1371/journal.pcbi.1007293 | Expression, Transcription, RNA-Seq, NGS/HTS, LINE/Non-LTR Retrotransposon, Activity, Short Read | Present (Dec 01 2025) | |
| Tedna | https://doi.org/10.1093/bioinformatics/btu365 | Assembly, Illumina, Paired-End, NGS/HTS | Present (Dec 01 2025) | |
| Telescope | https://doi.org/10.1371/journal.pcbi.1006453 | Expression, Transcription, RNA-Seq | Present (Dec 01 2025) | |
| The RIPper | https://doi.org/10.7717/peerj.7447 | Link | RIP/Repeat-Induced Point Mutation, Mutation, GC, Repeat, Web Server | Present (Dec 01 2025) |
| TideHunter | https://doi.org/10.1093/bioinformatics/btz376 | Long Read, Tandem Repeat, NGS/HTS | Present (Dec 01 2025) | |
| TinT (Transposition in Transposition) | https://doi.org/10.1186/1471-2148-10-376 | Nested Insertion, Web Server | Present (Dec 01 2025) | |
| Tinscan | Comparative, Polymorphism, Genotype | Present (Dec 01 2025) | ||
| Tn-Core | https://doi.org/10.1021/acssynbio.8b00432 | Tn-Seq, Transposon Mutagenesis, RNA-Seq, Metabolic Modelling | Present (Dec 01 2025) | |
| Tn-seq Explorer | https://doi.org/10.1371/journal.pone.0126070 | Tn-Seq, Transposon Mutagenesis | Present (Dec 01 2025) | |
| Tn3+TA_finder | https://doi.org/10.1128/mBio.00452-20 | Transposon, Toxin-Antitoxin Loci | Present (Dec 01 2025) | |
| Tn3_finder | https://doi.org/10.1128/mBio.00452-20 | Transposon | Absent (Dec 01 2025) | |
| TnComp_finder | Composite Transposon | Absent (Dec 01 2025) | ||
| TnPred | http://dx.doi.org/10.1155/2012/678761 | Web Server, Transposase, Archaea, Bacteria, IS Element | Absent (Dec 01 2025) | |
| TopHat-Fusion | https://doi.org/10.1186/gb-2011-12-8-r72 | RNA-Seq, Transcription, Expression, Fusion | Present (Dec 01 2025) | |
| TrEMOLO | https://doi.org/10.1101/2022.07.21.500944 | NGS/HTS, Long Read, Oxford Nanopore, Genotype, Polymorphism | Present (Dec 01 2025) | |
| TraDIS toolkit | https://doi.org/10.1093/bioinformatics/btw022 | Tn-Seq, Transposon Mutagenesis | Present (Dec 01 2025) | |
| TraFIC | https://doi.org/10.1126/science.1251343 | NGS/HTS, Paired-End, Homo sapiens, Genotype, Polymorphism | Present (Dec 01 2025) | |
| TranSurVeyor | https://doi.org/10.1093/nar/gky685 | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (Dec 01 2025) | |
| TranspoScope | https://doi.org/10.1093/bioinformatics/btaa244 | Genotype, Polymorphism, Visualization, NGS/HTS | Present (Dec 01 2025) | |
| Transposeq | https://doi.org/10.1101/gr.163659.113 | Polymorphism, Genotype, Web Server, Homo sapiens, Eukaryotic Retrotransposon | Absent (Dec 01 2025) | |
| Transposome | https://doi.org/10.1093/bioinformatics/btv059 | De Novo, Assembly, Homology | Present (Dec 01 2025) | |
| Transposon Cluster Finder | https://doi.org/10.1371/journal.pcbi.0030137 | Nested Insertion | Absent (Dec 01 2025) | |
| TransposonPSI | BLAST, Eukaryotic Transposon | Present (Dec 01 2025) | ||
| TransposonUltimate | https://doi.org/10.1093/nar/gkac136 | Link | Eukaryotic Transposon, Library Generation, Classification, Annotation, Structural Variation | Present (Dec 01 2025) |
| TrustTEr | https://doi.org/10.1101/2020.07.07.191668 | RNA-Seq, Expression | ||
| TypeTE | https://doi.org/10.1093/nar/gkaa074 | Genotype, Polymorphism | Present (Dec 01 2025) | |
| UCSC Repeat Browser | https://doi.org/10.1101/429613 | Repeat, Visualization, Annotation | Present (Dec 01 2025) | |
| ULTRA | https://doi.org/10.1145/3233547.3233604 | Tandem Repeat, HMM, Repeat Masking | Present (Dec 01 2025) | |
| V-ELMpiRNAPred | https://doi.org/10.1142/S0219720016500463 | piRNA, Neural Network | Absent (Dec 01 2025) | |
| VHICA | https://doi.org/10.1093/molbev/msv341 | Horizontal Transfer | Present (Dec 01 2025) | |
| VISMapper | https://doi.org/10.1186/s12859-017-1837-z | Virus, NGS/HTS, Web Server, Genotype, Polymorphism, Insertion Site, Visualization | Present (Dec 01 2025) | |
| VRprofile | https://doi.org/10.1093/bib/bbw141 | Virulence, AMR/Antibiotic Resistance | Present (Dec 01 2025) | |
| VRprofile2 | https://doi.org/10.1093/nar/gkac321 | Virulence, AMR/Antibiotic Resistance | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| VirusSeq | https://doi.org/10.1093/bioinformatics/bts665 | Virus, RNA-Seq, Homo sapiens | Present (Dec 01 2025) | |
| VirusTaxo | https://doi.org/10.1101/2021.04.29.442004 | Virus, K-mer, Classification, Web Server | Present (Dec 01 2025) | |
| VisualRepbase | https://doi.org/10.1186/1471-2105-9-345 | Annotation, Visualization | Absent (Dec 01 2025) | |
| VisualTE | https://doi.org/10.1186/s12864-015-1351-5 | Annotation, Visualization | ||
| Vmatch | Repeat Annotation | Present (Dec 01 2025) | ||
| WGSSAT | https://doi.org/10.1093/jhered/esx075 | Simple Sequence Repeat/Microsatellite, Repeat Annotation, Primer | Present (Dec 01 2025) | |
| WindowMasker | https://doi.org/10.1093/bioinformatics/bti774 | Repeat Masking, Annotation, De Novo | Present (Dec 01 2025) | |
| Winnowmap2 | https://doi.org/10.1101/2020.11.01.363887 | Long Read, NGS/HTS, Repeat | Present (Dec 01 2025) | |
| WtP (What the Phage) | https://doi.org/10.1101/2020.07.24.219899 | Prophage/Bacteriophage, Annotation, Classification, Pipeline | Present (Dec 01 2025) | |
| YASS | https://doi.org/10.1093/nar/gki478 | Dot Plot, Visualization, Alignment, Web Server | Present (Dec 01 2025) | |
| YORO | https://doi.org/10.1371/journal.pone.0291925 | Classification, LTR Retrotransposon, Convolutional Neural Network | Present (Dec 01 2025) | |
| Zisland Explorer | https://doi.org/10.1093/bib/bbw019 | Genomic Island, GC | Absent (Dec 01 2025) | |
| alu-detect | https://doi.org/10.1093/nar/gkt612 | Alu, SINE, Genotype, Polymorphism, NGS/HTS, Paired-End | Present (Dec 01 2025) | |
| atena | http://52.71.54.154/packages/devel/bioc/html/atena.html | Pipeline, Expression, Transcription, RNA-Seq | Present (Dec 01 2025) | |
| binary_plus_multi_clasification.py | https://doi.org/10.7717/peerj.11456 | Classification, LTR Retrotransposon, K-mer | Present (Dec 01 2025) | |
| breseq | https://doi.org/10.1186/1471-2164-15-1039 | Structural Variation, Polymorphism, Genotype | Absent (Dec 01 2025) | |
| collapse_RepeatMasker_annotation | https://doi.org/10.1007/978-1-0716-2380-0_21 | Annotation | Present (Dec 01 2025) | |
| de_novo-identification | https://doi.org/10.13140/RG.2.2.27068.69765 | De Novo, Eukaryotic Transposon | Present (Dec 01 2025) | |
| detectIR | https://doi.org/10.1371/journal.pone.0113349 | Inverted Repeat | Present (Dec 01 2025) | |
| detectMITE | https://doi.org/10.1038/srep19688 | Library Generation, MITE, ITR/TIR/DNA Transposon | Present (Dec 01 2025) | |
| detettore | https://doi.org/10.1111/nph.16308 | Polymorphism, Genotype, NGS/HTS, Paired-End | Present (Dec 01 2025) | |
| digIS | https://doi.org/10.1186/s12859-021-04177-6 | IS Element, HMM | Present (Dec 01 2025) | |
| dimorphicERV | https://doi.org/10.1186/s13100-018-0142-3 | NGS/HTS, Short Read, Genotype, Polymorphism, ERV/Endogenous Retrovirus | Present (Dec 01 2025) | |
| discord-retro | https://arxiv.org/abs/1501.04268 | Illumina, Paired-End, NGS/HTS, Polymorphism, Genotype | Present (Dec 01 2025) | |
| dnaPipeTE | https://doi.org/10.1093/gbe/evv050 | GitHub | NGS/HTS, Assembly, Annotation | Present (Dec 01 2025) |
| dnaasm | https://doi.org/10.7490/f1000research.1114626.1 | Repeat, NGS/HTS, De Novo | Present (Dec 01 2025) | |
| dotmatcher | http://embossgui.sourceforge.net/demo/manual/dotmatcher.html | Dot Plot, Visualization | Present (Dec 01 2025) | |
| dotplot | Dot Plot, Visualization | Present (Dec 01 2025) | ||
| geNomad | https://doi.org/10.1038/s41587-023-01953-y | Virus, Plasmid, Machine Learning, Detection, Classification | Present (Dec 01 2025) | |
| iMGEins | https://doi.org/10.1186/s12864-018-5290-9 | NGS/HTS, Paired-End, Homology, Genotype, Polymorphism, Annotation | Present (Dec 01 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 (Dec 01 2025) | |
| iMapper | https://doi.org/10.1093/bioinformatics/btn541 | Genome, Ensembl, Transposon Mutagenesis | Present (Dec 01 2025) | |
| iSVP | https://doi.org/10.1186/1752-0509-7-s6-s8 | Structural Variation, Pipeline | Present (Dec 01 2025) | |
| inGAP-sv | https://doi.org/10.1093/nar/gkr506 | Structural Variation, NGS/HTS, Bayesian, Paired-End, Visualization | Present (Dec 01 2025) | |
| ltr.pl | https://doi.org/10.1186/1471-2164-8-90 | De Novo, LTR Retrotransposon, HMM | Absent (Dec 01 2025) | |
| mSINGS | https://doi.org/10.1373/clinchem.2014.223677 | Simple Sequence Repeat/Microsatellite, Instability, Polymorphism, Genotype, NGS/HTS, Cancer | Present (Dec 01 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 | Present (Dec 01 2025) |
| mge-cluster | https://doi.org/10.1101/2022.12.16.520696 | Link | Plasmid, Classification | Present (Dec 01 2025) |
| micRocounter | https://doi.org/10.1534/g3.119.400335 | Simple Sequence Repeat/Microsatellite, Annotation | Present (Dec 01 2025) | |
| mosaicFlye | https://doi.org/10.1101/2020.01.15.908285 | NGS/HTS, Long Read, Mosaic Repeat, Segmental Duplication, Assembly | Present (Dec 01 2025) | |
| mreps | https://doi.org/10.1093/nar/gkg617 | Tandem Repeat, De Novo, Library Generation | Present (Dec 01 2025) | |
| msatcommander | https://doi.org/10.1111/j.1471-8286.2007.01884.x | Simple Sequence Repeat/Microsatellite, Primer | Present (Dec 01 2025) | |
| msatfinder | Link | Simple Sequence Repeat/Microsatellite, Primer, Annotation, Repeat Extraction | Present (Dec 01 2025) | |
| nanomonsv | https://doi.org/10.1101/2020.07.22.214262 | Structural Variation, NGS/HTS, Long Read, Cancer | Present (Dec 01 2025) | |
| nanotei | https://doi.org/10.3390/plants10122681 | NGS/HTS, Oxford Nanopore, Polymorphism, Genotype | Present (Dec 01 2025) | |
| ncRNAclassifier | https://doi.org/10.1186/1471-2105-13-246 | ncRNA, miRNA | Present (Dec 01 2025) | |
| nf-repeatmasking | http://doi.org/10.5281/zenodo.1134750 | Repeat Masking, Classification | Present (Dec 01 2025) | |
| ngs_te_mapper | https://doi.org/10.1371/journal.pone.0030008 | Target Site Duplication, Homology, NGS/HTS | Present (Dec 01 2025) | |
| ntHits | https://doi.org/10.1371/journal.pone.0030008 | K-mer, Repeat | Present (Dec 01 2025) | |
| oriTfinder | https://doi.org/10.1093/nar/gky352 | Origin of Transfer, Plasmid, ICE/Integrative and Conjugative Element | Present (Dec 01 2025) | |
| packFinder | https://doi.org/10.1101/2021.06.18.448592 | Link | ITR/TIR/DNA Transposon, MuDR/Mutator, Pack-MULE | Present (Dec 01 2025) |
| panGRP | https://doi.org/10.1093/bioinformatics/btaa792 | Genomic Island | Present (Dec 01 2025) | |
| panHiTE | https://doi.org/10.1101/2025.02.15.638472 | Insertion Polymorphism, Polymorphism, Pangenome | Present (Dec 01 2025) | |
| panISa | https://doi.org/10.1093/bioinformatics/bty479 | De Novo, IS Element, NGS/HTS, Short Read, Annotation, Homology | Present (Dec 01 2025) | |
| phRAIDER | https://doi.org/10.1093/bioinformatics/btw258 | De Novo, Library Generation | Present (Dec 01 2025) | |
| piPipes | https://doi.org/10.1093/bioinformatics/btu647 | piRNA, RNA-Seq, ChIP-Seq, NGS/HTS | Present (Dec 01 2025) | |
| piRNA Pipeline | https://doi.org/10.1093/nar/gky761 | piRNA, NGS/HTS | Present (Dec 01 2025) | |
| piRNAPredictor | https://doi.org/10.1186/s12859-016-1206-3 | piRNA, Prediction | Present (Dec 01 2025) | |
| piRNN | https://doi.org/10.7717/peerj.5429 | piRNA, K-mer, Convolutional Neural Network | Present (Dec 01 2025) | |
| piRPred | https://doi.org/10.1093/bioinformatics/btu441 | piRNA, SVM | Present (Dec 01 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 (Dec 01 2025) | |
| polymorphicHERV | https://doi.org/10.1371/journal.pcbi.1006564 | ERV/Endogenous Retrovirus, K-mer, Genotype, Polymorphism, NGS/HTS | Present (Dec 01 2025) | |
| proTRAC | https://doi.org/10.1186/1471-2105-13-5 | piRNA | Absent (Dec 01 2025) | |
| rCANID | https://doi.org/10.1109/TNB.2019.2908438 | Long Read, NGS/HTS, Genotype, Polymorphism, Structural Variation | Present (Dec 01 2025) | |
| rMETL | https://doi.org/10.1093/bioinformatics/btz106 | Long Read, NGS/HTS, Genotype, Polymorphism | Present (Dec 01 2025) | |
| rMFilter | https://doi.org/10.1093/bioinformatics/btx279 | NGS/HTS, Structural Variation, Long Read | Present (Dec 01 2025) | |
| rTea (RNA-based Transposable Element Analyzer) | https://doi.org/10.1101/2023.10.16.562422 | RNA-Seq, Transcription, Expression, Fusion | Present (Dec 01 2025) | |
| rampage_alu | https://doi.org/10.1101/gr.249789.119 | RNA-Seq, Expression, Alu, SINE, RAMPAGE, NGS/HTS, Paired-End | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) | |
| repeatR | Eukaryotic Transposon, RepeatMasker, Annotation, Summary | Present (Dec 01 2025) | ||
| reputils | Github | TE Identification, Alignment, MSA, Manual Curation | Present (Dec 01 2025) | |
| retroSeeker | https://doi.org/10.1007/s44307-023-00005-5 | Eukaryotic Retrotransposon, Detection, Homology | Present (Dec 01 2025) | |
| retrotransposons-spread | https://doi.org/10.1093/bioinformatics/btw622 | Simulation, LTR Retrotransposon | Present (Dec 01 2025) | |
| sRNAPipe | https://doi.org/10.1186/s13100-018-0130-7 | Small RNA, RNA-Seq, Annotation | Present (Dec 01 2025) | |
| sRNAplot | https://doi.org/10.1038/s41559-017-0403-4 | Small RNA, piRNA, Visualization | Present (Dec 01 2025) | |
| sTELLeR | https://doi.org/10.1093/bioinformatics/btae686 | Long Read, Insertion Polymorphism, Polymorphism | Present (Dec 01 2025) | |
| scTE | https://doi.org/10.1038/s41467-021-21808-x | Single-Cell, RNA-Seq, Expression, Eukaryotic Transposon | Present (Dec 01 2025) | |
| sideRETRO | https://doi.org/10.1101/2020.03.09.983858 | Pseudogene, CNV/Copy Number Variation, Genotype, Polymorphism, NGS/HTS | Present (Dec 01 2025) | |
| sompop | https://doi.org/10.1093/bioinformatics/btaa279 | LINE1, LINE/Non-LTR Retrotransposon, Simulation, Cancer | Present (Dec 01 2025) | |
| somrit | https://www.biorxiv.org/content/10.1101/2023.08.06.552193v2.full.pdf | Retrotransposon, Insertion Polymorphism, Somatic, Mosaicism | Present (Dec 01 2025) | |
| starfish | https://doi.org/10.1101/2023.10.24.563810 | Starship, Tyrosine Recombinase, Detection, Annotation | Present (Dec 01 2025) | |
| svaRetro | https://doi.org/10.46471/gigabyte.70 | Structural Variation, Pseudogene, Expression, Transcription, LINE/Non-LTR Retrotransposon | Present (Dec 01 2025) | |
| svclassify | https://doi.org/10.1186/s12864-016-2366-2 | Structural Variation, Clustering, Classification | Present (Dec 01 2025) | |
| svviz2 | https://doi.org/10.1093/bioinformatics/btv478 | Structural Variation, Visualization | Present (Dec 01 2025) | |
| 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 (Dec 01 2025) |
| tantan | https://doi.org/10.1093/nar/gkq1212 | Repeat, Repeat Masking | Absent (Dec 01 2025) | |
| tek2 | https://doi.org/10.1093/molbev/msz220 | Simulation, Genome, Divergence, Evolution | Present (Dec 01 2025) | |
| tephra | Homology, Library Generation, Structure, Classification, Age, Annotation | Present (Dec 01 2025) | ||
| vHULK (Viral Host UnveiLing Kit) | https://doi.org/10.1101/2020.12.06.413476 | Prophage/Bacteriophage | Present (Dec 01 2025) | |
| xTea | https://doi.org/10.1038/s41467-021-24041-8 | Eukaryotic Transposon, Polymorphism, Genotype, Long Read, Short Read, Pangenome | Present (Dec 01 2025) | |
| xenoGI | https://doi.org/10.1186/s12859-018-2038-0 | Genomic Island, Synteny, Phylogeny | Present (Dec 01 2025) |