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