This page compiles a list of software for the detection, annotation, analysis, simulation and visualization of repetitive, mobile and selfish DNA and related entities.
It is maintained by Tyler A. Elliott. It was initiated with the help of Elizabeth Smikle and Miduna Rahulan, formerly at the Centre for Biodiversity Genomics at the University of Guelph. Suggestions, updates and error corrections are welcome. Please feel free to add missing tools into the table, that would help a lot!
For resources more tailored to Prokaryotes and Viruses (as well as here and here), see the linked lists.
We encourage the authors of these tools to create pages for them on TE Hub, so that they can provide more information about their work, and link it back to this table. Please find a template software sheet here.
| Tool | DOI | Alternate URL | Keywords | Status |
|---|---|---|---|---|
| 2lpiRNApred | https://doi.org/10.1080/15476286.2020.1734382 | piRNA | Present (Aug 05 2024) | |
| 2-n-way Genome Suite | https://doi.org/10.1101/gr.262261.120 | Polymorphism, Genotype, Webserver | Present (Aug 05 2024) | |
| 4-LIN | https://doi.org/10.1093/sysbio/syac082 | Web Server, Phylogeny, Eukaryotic Retrotransposon | Absent (Aug 05 2024) | |
| AAARF (Assisted Automated Assembler of Repeat Families) | https://doi.org/10.1186/1471-2105-9-235 | Homology, Alignment | Present (Aug 05 2024) | |
| AgIn | https://doi.org/10.1093/bioinformatics/btw360 | PacBio, Methylation | Present (Aug 05 2024) | |
| AlbaTraDIS | https://doi.org/10.1371/journal.pcbi.1007980 | Tn-Seq, Transposon Mutagenesis | Present (Aug 05 2024) | |
| Alien_Hunter | https://doi.org/10.1093/bioinformatics/btl369 | Genomic Island, HMM | Absent (Aug 05 2024) | |
| alu-detect | https://doi.org/10.1093/nar/gkt612 | Alu, SINE, Genotype, Polymorphism, NGS/HTS, Paired-End | Present (Aug 05 2024) | |
| AluMine | https://doi.org/10.1101/588434 | Alu, SINE, Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| Alpha-CENTAURI | https://doi.org/10.1093/bioinformatics/btw101 | Satellite, Centromere, Tandem Repeat, HMM, Long-Read | Present (Aug 05 2024) | |
| AnnoSINE | https://doi.org/10.1093/plphys/kiab524 | SINE, Annotation, HMM | Present (Aug 05 2024) | |
| AnTE | https://doi.org/10.1371/journal.pgen.1004482 | Simulation, Phylogeny, Bayesian MCMC, Ancestral Reconstruction | Absent (Aug 05 2024) | |
| ANUBIS | https://doi.org/10.1093/nar/gkaa679 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism, Visualization | Present (Aug 05 2024) | |
| ARTIST | https://doi.org/10.1371/journal.pgen.1004782 | Tn-Seq, Transposon Mutagenesis, HMM | Present (Aug 05 2024) | |
| atena | http://52.71.54.154/packages/devel/bioc/html/atena.html | Pipeline, Expression, Transcription, RNA-Seq | Present (Aug 05 2024) | |
| Attacca | https://doi.org/10.1186/1471-2105-10-281 | Integron | ||
| BacAnt | https://doi.org/10.3389/fmicb.2021.649969 | Link | IS Element, Archaeal/Bacterial Transposon, Integron, AMR/Antibiotic Resistance, Annotation, Web Server | Present (Aug 05 2024) |
| Bakta | https://doi.org/10.1099/mgen.0.000685 | Link | Metagenomics, Annotation | Present (Aug 05 2024) |
| Bellerophon | https://doi.org/10.1186/1471-2105-14-s5-s6 | Structural Variation, NGS/HTS, Paired-End | ||
| binary_plus_multi_clasification.py | https://doi.org/10.7717/peerj.11456 | Classification, LTR Retrotransposon, K-mer | Present (Aug 05 2024) | |
| BLATCAT | https://doi.org/10.1155/2014/730814 | BLAT, Homology | ||
| BreakDancer | https://doi.org/10.1038/nmeth.1363 | Structural Variation, NGS/HTS, Short-Read, Paired-End, MAQ | Absent (Aug 05 2024) | |
| breseq | https://doi.org/10.1186/1471-2164-15-1039 | Structural Variation, Polymorphism, Genotype | Absent (Aug 05 2024) | |
| 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 (Aug 05 2024) | |
| CAFE (Coefficient-based Analysis of Fitness by read Enrichments) | https://doi.org/10.1093/bioinformatics/btaa1086 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (Aug 05 2024) | |
| CAULIFINDER | https://doi.org/10.1186/s13100-022-00288-w | Detection, Annotation, EVE, Plants, Virus | Present (Aug 05 2024) | |
| CAlu Alu Classifier | https://doi.org/10.1016/j.cell.2010.05.020 | Genotype, Polymorphism, Homo sapiens, Alu, SINE, Web Server | Absent (Aug 05 2024) | |
| CARP | https://doi.org/10.1371/journal.pone.0193588 | De Novo, Library Generation, Homology, Annotation | Present (Aug 05 2024) | |
| CELLO-Seq (single CELl LOng read RNA sequencing) | https://doi.org/10.1101/2020.10.02.322073 | Single Cell, RNA-Seq, Eukaryotic Transposon | Present (Aug 05 2024) | |
| Censor | https://doi.org/10.1016/S0097-8485(96)80013-1 | Annotation, Repeat Masking | Present (Aug 05 2024) | |
| CGS | https://doi.org/10.1186/1471-2164-13-245 | Horizontal Transfer, K-mer | ||
| ChimeraTE | https://doi.org/10.1093/nar/gkad671 | RNA-Seq, Expression, Transcription, Paired-End, NGS/HTS, Chimera | Present (Aug 05 2024) | |
| CIAlign | https://doi.org/10.7717/peerj.12983 | Alignment, MSA, Manual Curation | Present (Aug 05 2024) | |
| CLARI-TE | https://doi.org/10.1186/s13059-014-0546-4 | Homology, Annotation, Nested Insertion | Present (Aug 05 2024) | |
| ClassifyTE | https://doi.org/10.1093/bioinformatics/btab146 | Classification, Eukaryotic Transposon | Present (Aug 05 2024) | |
| CLIFinder | https://doi.org/10.1093/bioinformatics/btx671 | LINE1, Transcription, RNA-Seq, Expression, Chimera, NGS/HTS | Present (Aug 05 2024) | |
| CLOVE | https://doi.org/10.1186/s12859-017-1760-3 | Structural Variation | Present (Aug 05 2024) | |
| ClustAGE | https://doi.org/10.1186/s12859-018-2154-x | Comparative, BLAST, Archaea, Bacteria | Present (Aug 05 2024) | |
| collapse_RepeatMasker_annotation | https://doi.org/10.1007/978-1-0716-2380-0_21 | Annotation | Present (Aug 05 2024) | |
| COLOMBO | https://doi.org/10.1186/1471-2105-7-142 | Genomic Island, Codon Usage, HMM | Present (Aug 05 2024) | |
| CompTIS | https://doi.org/10.1128/mSphere.00031-19 | Tn-Seq, Transposon Mutagenesis, PCA | Present (Aug 05 2024) | |
| CONJscan | https://doi.org/10.1007/978-1-4939-9877-7_19 | Plasmid, ICE/Integrative and Conjugative Element | Present (Aug 05 2024) | |
| ConTExt | https://genome.cshlp.org/content/28/5/714 | Illumina, Paired-End, Homology, NGS/HTS, Polymorphism | Present (Aug 05 2024) | |
| COSEG | Subfamily Identification, Eukaryotic Transposon, Alu, SINE | Present (Aug 05 2024) | ||
| ConsensusSV | https://doi.org/10.1093/bioinformatics/btac709 | NGS/HTS, Short Read, Illumina, Structural Variation | Present (Aug 05 2024) | |
| COPLA | https://doi.org/10.1101/2020.12.15.422809 | Plasmid, Classification, Homology | Present (Aug 05 2024) | |
| CRISPRCasTyper | https://doi.org/10.1101/2020.05.15.097824 | Link | CRISPR, Classification, Annotation | Present (Aug 05 2024) |
| DANTE | Link | Homology, Library Generation | Present (Aug 05 2024) | |
| DAWG-PAWS | https://doi.org/10.1186/1746-4811-5-8 | Homology, HMM, Annotation, Gene Prediction | Present (Aug 05 2024) | |
| DarkHorse | https://doi.org/10.1186/gb-2007-8-2-r16 | Horizontal Transfer, Homology, Phylogeny | Absent (Aug 05 2024) | |
| 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 (Aug 05 2024) | |
| DARTS (Domain-Associated RetroTransposon Search) | https://doi.org/10.1101/2021.12.03.471067 | Pipeline, Homology, Annotation, Retrotransposon | Present (Aug 05 2024) | |
| DBSCAN-SWA | https://doi.org/10.1101/2020.07.12.199018 | Prophage/Bacteriophage, Homology | Present (Aug 05 2024) | |
| DD-Detection | https://doi.org/10.1093/bioinformatics/btv621 | NGS/HTS, Illumina, Paired-End, Polymorphism | Present (Aug 05 2024) | |
| D-Genies | https://doi.org/10.7717/peerj.4958 | Dot Plot, Visualization | Present (Aug 05 2024) | |
| DeBreak | https://doi.org/10.21203/rs.3.rs-1261915/v1 | NGS/HTS, Long-Read, Structural Variation | Present (Aug 05 2024) | |
| DeepMEI | https://doi.org/10.1101/2023.03.07.531451 | NGS/HTS, Short Read, Genotype, Polymorphism, Convolutional Neural Network | Present (Aug 05 2024) | |
| DeepRepeat | https://doi.org/10.1186/s13059-022-02670-6 | NGS/HTS, Short Tandem Repeat, Long-Read, Oxford Nanopore | Present (Aug 05 2024) | |
| DeepTE | https://doi.org/10.1093/bioinformatics/btaa519 | Classification, Convolutional Neural Network | Present (Aug 05 2024) | |
| Delly | https://doi.org/10.1093/bioinformatics/bts378 | Structural Variation, NGS/HTS, Short-Read, Paired-End | Present (Aug 05 2024) | |
| de_novo-identification | https://doi.org/10.13140/RG.2.2.27068.69765 | De Novo, Eukaryotic Transposon | Present (Aug 05 2024) | |
| DEPht | https://doi.org/10.1093/nar/gkac273 | Annotation, Extraction, Prophage/Bacteriophage | Present (Aug 05 2024) | |
| DeRIP | https://doi.org/10.1186/1471-2164-11-655 | RIP/Repeat-Induced Point Mutation, Prediction, Fungi | Present (Aug 05 2024) | |
| Design-Island | https://doi.org/10.1186/1471-2164-9-150 | Genomic Island, Monte-Carlo, GC, Codon Usage | ||
| detectIR | https://doi.org/10.1371/journal.pone.0113349 | Inverted Repeat | Present (Aug 05 2024) | |
| detectMITE | https://doi.org/10.1038/srep19688 | Library Generation, MITE, ITR/TIR/DNA Transposon | Present (Aug 05 2024) | |
| detettore | https://doi.org/10.1111/nph.16308 | Polymorphism, Genotype, NGS/HTS, Paired-End | Present (Aug 05 2024) | |
| DeviaTE | https://doi.org/10.1111/1755-0998.13030 | NGS/HTS, Abundance, Visualization, Divergence | Present (Aug 05 2024) | |
| DGRscan | https://doi.org/10.3390/ijms150814234 | DGR/Diversity Generating Retroelement, Annotation | Present (Aug 05 2024) | |
| digIS | https://doi.org/10.1186/s12859-021-04177-6 | IS Element, HMM | Present (Aug 05 2024) | |
| DiGReF | https://doi.org/10.1186/1471-2164-13-430 | DGR/Diversity Generating Retroelement, Annotation | Absent (Aug 05 2024) | |
| dimorphicERV | https://doi.org/10.1186/s13100-018-0142-3 | NGS/HTS, Short-Read, Genotype, Polymorphism, ERV/Endogenous Retrovirus | Present (Aug 05 2024) | |
| discord-retro | https://arxiv.org/abs/1501.04268 | Illumina, Paired-End, NGS/HTS, Polymorphism, Genotype | Present (Aug 05 2024) | |
| DIVE | https://doi.org/10.1101/2022.06.13.495703 | De Novo, K-mer, Repeat | Present (Aug 05 2024) | |
| dnaasm | https://doi.org/10.7490/f1000research.1114626.1 | Repeat, NGS/HTS, De Novo | Present (Aug 05 2024) | |
| Dna-brnn | https://doi.org/10.1093/bioinformatics/btz264 | Satellite, Centromere, Neural Network | Present (Aug 05 2024) | |
| dnaPipeTE | https://doi.org/10.1093/gbe/evv050 | GitHub | NGS/HTS, Assembly, Annotation | Present (Aug 05 2024) |
| Domain Organizer | https://doi.org/10.1093/bioinformatics/btl337 | Alignment, HMM, Domain, Visualization | Absent (Aug 05 2024) | |
| Dotlet | https://doi.org/10.1093/bioinformatics/16.2.178 | Dot Plot, Visualization | Present (Aug 05 2024) | |
| dotmatcher | http://embossgui.sourceforge.net/demo/manual/dotmatcher.html | Dot Plot, Visualization | Present (Aug 05 2024) | |
| dotplot | Dot Plot, Visualization | Present (Aug 05 2024) | ||
| Dotter | https://doi.org/10.1016/0378-1119(95)00714-8 | Visualization, Dot Plot | Present (Aug 05 2024) | |
| DTExpress | https://doi.org/10.1007/978-1-0716-1134-0_2 | RNA-Seq, Expression | Present (Aug 05 2024) | |
| Duster | https://peercommunityjournal.org/articles/10.24072/pcjournal.68/ | Library Generation, Homology, K-mer | Present (Aug 05 2024) | |
| Dysgu | https://doi.org/10.1093/nar/gkac039 | NGS/HTS, Short-Read, Long-Read, Structural Variation | Present (Aug 05 2024) | |
| EAHelitron | https://doi.org/10.1186/s12859-019-2945-8 | Helitron, Structure | Present (Aug 05 2024) | |
| EarlGrey | https://doi.org/10.21203/rs.3.rs-1812599/v1 | Pipeline, Annotation, Repeat Masking, Homology, De Novo, Library Generation | Present (Aug 05 2024) | |
| Easymap | https://doi.org/10.3389/fpls.2021.655286 | Link | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (Aug 05 2024) |
| Ecc_finder | https://www.frontiersin.org/articles/10.3389/fpls.2021.743742/abstract | essDNA, NGS/HTS, Oxford Nanopore | Present (Aug 05 2024) | |
| ECCsplorer | https://doi.org/10.1186/s12859-021-04545-2 | eccDNA, Identification, Active TEs | Present (Aug 05 2024) | |
| EDTA | https://doi.org/10.1186/s13059-019-1905-y | Library Generation, Filtering, Structure, De Novo | Present (Aug 05 2024) | |
| EGID | https://doi.org/10.6026/007/97320630007311 | Genomic Island, Prediction | Absent (Aug 05 2024) | |
| ELAN | https://doi.org/10.1093/nar/gkr337 | Homology, Insertion Site, Consensus | Absent (Aug 05 2024) | |
| ELITE (Efficiently Locating Insertions of Transposable Elements) | https://doi.org/10.1145/3307339.3342182 | Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| EpiTEome | https://doi.org/10.1186/s13059-017-1232-0 | Polymorphism, Genotype, NGS/HTS, Methyl-Seq, Bisulfite, Methylation, | Present (Aug 05 2024) | |
| ERVcaller | https://doi.org/10.1093/bioinformatics/btz205 | ERV/Endogenous Retrovirus, Homo sapiens, NGS/HTS, Polymorphism, Genotype | Absent (Aug 05 2024) | |
| ERVmap | https://doi.org/10.1073/pnas.1814589115 | ERV/Endogenous Retrovirus, RNA-Seq, Transcriptome,Homo sapiens | Present (Aug 05 2024) | |
| ESAP Plus | https://doi.org/10.1186/s12864-016-3328-4 | Simple Sequence Repeat/Microsatellite, Expression, EST, Clustering, Repeat Masking | Present (Aug 05 2024) | |
| ESMP | https://doi.org/10.6026/97320630008206 | Simple Sequence Repeat/Microsatellite, Expression, EST, Clustering | Absent (Aug 05 2024) | |
| ESSENTIALS | https://doi.org/10.1371/journal.pone.0043012 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Absent (Aug 05 2024) | |
| ExoPLOT | https://doi.org/10.1016/j.ygeno.2022.110434 | RNA-Seq, Expression, Transcription, NGS/HTS | Present (Aug 05 2024) | |
| ExpansionHunter | https://doi.org/10.1101/gr.225672.117 | Short Read, NGS/HTS, Short Tandem Repeat | Present (Aug 05 2024) | |
| ExpansionHunter Denovo | https://doi.org/10.1101/863035 | Short-Read, NGS/HTS, Short Tandem Repeat | Present (Aug 05 2024) | |
| ExplorATE | https://doi.org/10.1093/bioinformatics/btac354 | Expression, Transcription, RNA-Seq | Present (Aug 05 2024) | |
| FasTE | https://doi.org/10.1111/1755-0998.13489 | De Novo, Homology, Library Generation, Annotation, Pipeline, Classification | Present (Aug 05 2024) | |
| Fastq2LoxDel | https://doi.org/10.1101/2020.07.14.202044 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (Aug 05 2024) | |
| FASTQINS | https://doi.org/10.1093/nar/gkaa679 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism, Read Mapping | Present (Aug 05 2024) | |
| FindTelomeres | Telomere | Present (Aug 05 2024) | ||
| FiTnEss (Finding Tn-Seq Essentials) | https://doi.org/10.1073/pnas.1900570116 | Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism | Present (Aug 05 2024) | |
| FlexDotPlot | https://doi.org/10.1101/2020.04.03.023655 | Visualization, Dot Plot | Present (Aug 05 2024) | |
| FlexiDot | https://doi.org/10.1093/bioinformatics/bty395 | Visualization, Dot Plot | Present (Aug 05 2024) | |
| FORRepeats | https://doi.org/10.1093/bioinformatics/btf843 | Repeat, Detection | ||
| FullSSR | https://doi.org/10.1155/2016/6040124 | Simple Sequence Repeat/Microsatellite, Primer | Present (Aug 05 2024) | |
| GASVPro | https://doi.org/10.1186/gb-2012-13-3-r22 | Structural Variation, NGS/HTS,Paired-End | Absent (Aug 05 2024) | |
| GC-Profile | https://doi.org/10.2174/1389202915999140328163125 | Genomic Island, GC | Absent (Aug 05 2024) | |
| GeIST | https://doi.org/10.1093/bioinformatics/btv350 | Tn-Seq, Transposon Mutagenesis | Present (Aug 05 2024) | |
| Generic Repeat Finder | https://doi.org/10.1104/pp.19.00386 | LTR Retrotransposon, MITE, Inverted Repeat, ITR/TIR/DNA Transposon | Present (Aug 05 2024) | |
| GeneTEFlow | https://doi.org/10.1101/2020.04.28.065862 | RNA-Seq, NGS/HTS, Nextflow | Present (Aug 05 2024) | |
| geNomad | https://doi.org/10.1038/s41587-023-01953-y | Virus, Plasmid, Machine Learning, Detection, Classification | Absent (Aug 05 2024) | |
| Genome ARTIST v2 | https://doi.org/10.3390/ijms232012686 | Tn-Seq, Transposon Mutagenesis, Drosophila, ITR/TIR/DNA Transposon | Present (Aug 05 2024) | |
| GenomeDiff | Dot Plot, Visualization, Virus | Present (Aug 05 2024) | ||
| GenomeTools | https://doi.ieeecomputersociety.org/10.1109/TCBB.2013.68 | Genome Annotation | Present (Aug 05 2024) | |
| Gepard | https://doi.org/10.1093/bioinformatics/btm039 | Visualization, Dot Plot | Present (Aug 05 2024) | |
| G-IMEx | https://doi.org/10.6026/97320630005221 | Simple Sequence Repeat/Microsatellite, Repeat Extraction, Annotation | Absent (Aug 05 2024) | |
| GI-Cluster | https://doi.org/10.1142/S0219720018400103 | Genomic Island, GC, Codon Usage, K-mer | Present (Aug 05 2024) | |
| GIDetector | https://doi.org/10.1186/1471-2164-11-S2-S1 | Genomic Island, Pipeline | Absent (Aug 05 2024) | |
| GIHunter | https://doi.org/10.4172/jpb.1000322 | Genomic Island, Prediction | Absent (Aug 05 2024) | |
| GI-POP | https://doi.org/10.1016/j.gene.2012.11.063 | Genomic Island, SVM, Annotation | Absent (Aug 05 2024) | |
| GIPSy | https://doi.org/10.1016/j.jbiotec.2015.09.008 | Genomic Island, GC, Homology, HMM | Present (Aug 05 2024) | |
| GIST | https://doi.org/10.6026/97320630008203 | Genomic Island, Pipeline | Absent (Aug 05 2024) | |
| GI-SVM | https://doi.org/10.1142/S0219720016400035 | Genomic Island, SVM, K-mer | Present (Aug 05 2024) | |
| GIV | https://doi.org/10.6026/97320630009879 | Genomic Island, Visualization | Absent (Aug 05 2024) | |
| GMATA | https://doi.org/10.3389/fpls.2016.01350 | Simple Sequence Repeat/Microsatellite, Repeat Extraction, Annotation, Primer | Present (Aug 05 2024) | |
| GMATo | https://doi.org/10.6026/97320630009541 | Simple Sequence Repeat/Microsatellite, Repeat Annotation | Present (Aug 05 2024) | |
| GPAC (Genome Presence/Absence Compiler) | https://doi.org/10.1093/molbev/msu276 | Polymorphism, Genotype | Present (Aug 05 2024) | |
| GraffiTE | https://doi.org/10.1101/2023.09.11.557209 | Polymorphism, Structural Variation, Long-Read, NGS/HTS, Assemblies, Pangenomes, Graph-Genome, Genotype | Present (Aug 05 2024) | |
| GraphTyper | https://doi.org/10.1038/ng.3964 | Structural Variation, Short-Read, NGS/HTS | Present (Aug 05 2024) | |
| GraphTyper2 | https://doi.org/10.1038/s41467-019-13341-9 | Structural Variation, Short-Read, NGS/HTS | Present (Aug 05 2024) | |
| GRASPER | https://doi.org/10.1089/cmb.2013.0129 | Structural Variation, Repeat, Homology, NGS/HTS, Paired-End | Present (Aug 05 2024) | |
| GREAM | https://doi.org/10.1371/journal.pone.0133647 | Mammal, Web Server,Genome, Analysis | Present (Aug 05 2024) | |
| Greedier | https://doi.org/10.1093/bioinformatics/btm613 | Homology, Repeat Masking,Nested Insertion, Graph | Present (Aug 05 2024) | |
| HashRepeatFinder | https://doi.org/10.1007/s12539-015-0119-6 | De Novo, Library Generation | Absent (Aug 05 2024) | |
| HDRSM (Highly Divergent Repeat Search Method) | https://doi.org/10.1186/s12859-021-03977-0 | SINE | Present (Aug 05 2024) | |
| HELIANO | https://doi.org/10.1101/2024.02.08.579435 | Helitron, Annotation | Present (Aug 05 2024) | |
| HelitronFinder | https://doi.org/10.1186/1471-2164-9-51 | Helitron, Structure | Absent (Aug 05 2024) | |
| HelitronScanner | https://doi.org/10.1073/pnas.1410068111 | Helitron, Structure | Present (Aug 05 2024) | |
| HelSearch | https://doi.org/10.1073/pnas.0905563106 | Helitron, Structure | Present (Aug 05 2024) | |
| HERA (Highly Efficient Repeat Assembly) | https://doi.org/10.1038/s41467-019-13355-3 | Long-Read, Graph, Assembly | ||
| HiC-TE | https://doi.org/10.1101/2021.12.18.473300 | Hi-C, NGS/HTS, Pipeline | Present (Aug 05 2024) | |
| HiTE | https://doi.org/10.1101/2023.05.23.541879 | Detection, Annotation | Present (Aug 05 2024) | |
| HiTea | https://doi.org/10.1101/2020.04.27.060145 | Hi-C, NGS/HTS, Genotype, Polymorphism | Present (Aug 05 2024) | |
| HIVIntact | https://doi.org/10.1186/s12977-021-00561-5 | Retrovirus, Activity | Present (Aug 05 2024) | |
| HMMER | https://doi.org/10.1371/journal.pcbi.1000069 | HMM | Present (Aug 05 2024) | |
| HomologMiner | https://doi.org/10.1093/bioinformatics/btm048 | Homology, Genome, Comparative | Absent (Aug 05 2024) | |
| HTdetect | https://doi.org/10.1093/gbe/evu026 | Horizontal Transfer, Homology | Present (Aug 05 2024) | |
| ICEfinder | https://doi.org/10.1093/nar/gky1123 | Link | ICE/Integrative and Conjugative Element, HMM | Present (Aug 05 2024) |
| ICEscreen | https://doi.org/10.1093/nargab/lqac079 | ICE/Integrative and Conjugative Element, HMM | Present (Aug 05 2024) | |
| IDSSR | https://doi.org/10.3390/ijms20143497 | Simple Sequence Repeat/Microsatellite, NGS/HTS, Paired-End, Primer, Repeat Annotation, Polymorphism | Present (Aug 05 2024) | |
| IGIPT | https://doi.org/10.6026/007/97320630007307 | Genomic Island, Nucleotide Composition, Visualization | Present (Aug 05 2024) | |
| iMapper | https://doi.org/10.1093/bioinformatics/btn541 | Genome, Ensembl, Transposon Mutagenesis | Present (Aug 05 2024) | |
| IMEx | https://doi.org/10.1093/bioinformatics/btm097 | Simple Sequence Repeat/Microsatellite, Annotation, Web Server | Absent (Aug 05 2024) | |
| iMGEins | https://doi.org/10.1186/s12864-018-5290-9 | NGS/HTS, Paired-End, Homology, Genotype, Polymorphism, Annotation | Present (Aug 05 2024) | |
| iMSAT | https://doi.org/10.1186/1471-2164-15-858 | Simple Sequence Repeat/Microsatellite, Illumina, NGS/HTS, Short-Read, Genotype, Polymorphism, Repeat Extraction | Present (Aug 05 2024) | |
| INDeGenIUS | https://doi.org/10.1007/s12038-010-0040-4 | Genomic Island, K-mer | ||
| inGAP-sv | https://doi.org/10.1093/nar/gkr506 | Structural Variation, NGS/HTS, Bayesian, Paired-End, Visualization | Present (Aug 05 2024) | |
| InFire | https://doi.org/10.1093/bioinformatics/btr672 | Transposon Mutagenesis, Web Server,Restriction Digestion | Absent (Aug 05 2024) | |
| InMut-Finder | https://doi.org/10.1186/s12864-021-08206-9 | NGS/HTS, Onxford Nanopore, Tn-Seq, Transposon Mutagenesis | Present (Aug 05 2024) | |
| Inpactor | https://doi.org/10.3390/biology7020032 | LTR Retrotransposon, Classification, Insertion Time | Present (Aug 05 2024) | |
| Inpactor2 | https://doi.org/10.1093/bib/bbac511 | LTR Retrotransposon, Classification, Insertion Time, Neural Network | Present (Aug 05 2024) | |
| InsertionMapper | https://doi.org/10.1186/1471-2164-14-679 | Tn-Seq, Transposon Mutagenesis, NGS/HTS | Present (Aug 05 2024) | |
| In-seq/Tn-seq | http://doi.org/10.1038/nprot.2011.417 | Tn-Seq, Transposon Mutagenesis | Present (Aug 05 2024) | |
| INSurVeyor | https://doi.org/10.1038/s41467-023-38870-2 | Polymorphism, Short-Reads, NGS/HTS, Paired-End | Present (Aug 05 2024) | |
| IntegronFinder | https://doi.org/10.1093/nar/gkw319 | Link | Integron, HMM | Present (Aug 05 2024) |
| IntegronFinder 2.0 | https://doi.org/10.3390/microorganisms10040700 | Integron, HMM | Present (Aug 05 2024) | |
| Invade | https://doi.org/10.1093/molbev/msz079 | Simulation, piRNA, Genome | Present (Aug 05 2024) | |
| IpiRId | https://doi.org/10.1371/journal.pone.0179787 | piRNA, SVM | Absent (Aug 05 2024) | |
| IRescue | https://doi.org/10.1101/2022.09.16.508229 | Single-Cell, NGS/HTS, RNA-Seq, Expression, Transcription | Present (Aug 05 2024) | |
| IRF | https://doi.org/10.1101/gr.2542904 | Google drive link | Inverted Repeat, Library Generation | |
| IRplus | https://doi.org/10.1093/gbe/evad177 | Link | Inverted Repeat, Plastid, Webserver | Present (Aug 05 2024) |
| ISAbR_finder | IS Element, AMR/Antibiotic Resistance | Absent (Aug 05 2024) | ||
| ISCompare | https://doi.org/10.1093/g3journal/jkab181 | IS Element, Genotype, Polymorphism | Present (Aug 05 2024) | |
| IScan | https://doi.org/10.1093/nar/gkm597 | IS Element, Homology | Absent (Aug 05 2024) | |
| ISEScan | https://doi.org/10.1093/bioinformatics/btx433 | IS Element, HMM, Homology, Library Generation | Present (Aug 05 2024) | |
| IslandCafe | https://doi.org/10.1534/g3.119.400562 | Genomic Island | Present (Aug 05 2024) | |
| IslandPath-DIMOB | https://doi.org/10.1093/bioinformatics/bty095 | Genomic Island, HMM, Homology, K-mer | Present (Aug 05 2024) | |
| IslandPick | https://doi.org/10.1186/1471-2105-9-329 | Genomic Island, Homology, Comparative | Absent (Aug 05 2024) | |
| IslandViewer 4 | https://doi.org/10.1093/bioinformatics/btp030 | Genomic Island, Visualization, Web Server | Absent (Aug 05 2024) | |
| ISMapper | https://doi.org/10.1186/s12864-015-1860-2 | IS Element, Short-Read, NGS/HTS, Illumina, Paired-End, Polymorphism, Genotype | Present (Aug 05 2024) | |
| ISQuest | https://doi.org/10.1093/bioinformatics/btv388 | IS Element, NGS/HTS, Homology | Present (Aug 05 2024) | |
| ISsaga | https://doi.org/10.1186/gb-2011-12-3-r30 | Homology, Annotation, IS Element | Absent (Aug 05 2024) | |
| ISseeker | https://doi.org/10.1099/mgen.0.000062 | IS Element, Homology, Comparative | Present (Aug 05 2024) | |
| iSVP | https://doi.org/10.1186/1752-0509-7-s6-s8 | Structural Variation, Pipeline | Present (Aug 05 2024) | |
| ITIS (Identification of Transposon Insertion Sites) | https://doi.org/10.1186/s12859-015-0507-2 | Genotype, Polymorphism, NGS/HTS | Absent (Aug 05 2024) | |
| IUPACpal | https://doi.org/10.1186/s12859-021-03983-2 | Inverted Repeat | Present (Aug 05 2024) | |
| JDotter | https://doi.org/10.1093/bioinformatics/btg406 | Dot Plot, Visualization | Present (Aug 05 2024) | |
| Jitterbug | https://doi.org/10.1186/s12864-015-1975-5 | Paired-End, NGS/HTS, Polymorphism, Genotype, | Present (Aug 05 2024) | |
| KKSC Significance Test | https://doi.org/10.1371/journal.pcbi.1004812 | Polymorphism, Genotype, LINE/Non-LTR Retrotransposon, Age, Speciation | Present (Aug 05 2024) | |
| L1EM | https://doi.org/10.1093/bioinformatics/btz724 | Expression, Transcription, LINE1, LINE/Non-LTR Retrotransposon, Activity, NGS/HTS | Present (Aug 05 2024) | |
| L1PD (LINE-1 Pattern Detection) | https://doi.org/10.1186/s12859-022-04907-4 | LINE1, LINE/Non-LTR Retrotransposon, K-mer | Present (Aug 05 2024) | |
| L1Seq | https://doi.org/10.1101/gr.106419.110 | LINE/Non-LTR Retrotransposon, LINE1 | Present (Aug 05 2024) | |
| LAST | https://doi.org/10.1186/s13059-015-0670-9 | Alignment, Repeat | Absent (Aug 05 2024) | |
| LIONS | https://doi.org/10.1093/bioinformatics/btz130 | RNA-Seq, Transcription | Present (Aug 05 2024) | |
| LocaTR | https://doi.org/10.1186/s12864-016-3043-1 | LTR Retrotransposon, Homology, Structure, Annotation | Present (Aug 05 2024) | |
| LocusMasterTE | https://doi.org/10.1101/2023.03.21.533716 | NGS/HTS, Long-Read, Expression, Transcription, RNA-Seq | Present (Aug 05 2024) | |
| LongRepMarker | https://doi.org/10.1093/nar/gkab563 | De Novo, K-mer, Library Generation, Long-Read, Short-Read | Present (Aug 05 2024) | |
| Look4LTRs | https://doi.org/10.1186/s13100-024-00317-w | LTR Retrotransposon, Nested Insertion, Annotation | Present (Aug 05 2024) | |
| LoRTE | https://doi.org/10.1186/s13100-017-0088-x | Long-Read, PacBio, NGS/HTS, Genotype, Polymorphism, Indel,Homology | Absent (Aug 05 2024) | |
| LoRTIS-SS | https://doi.org/10.1101/2022.05.26.493556 | Long-Read, NGS/HTS, Oxford Nanopore, Tn-Seq, Transposon Mutagenesis | Present (Aug 05 2024) | |
| LTR_FINDER | https://doi.org/10.1093/nar/gkm286 | LTR Retrotransposon, Structure, Web Server | Absent (Aug 05 2024) | |
| LTR_FINDER_parallel | https://doi.org/10.1186/s13100-019-0193-0 | LTR Retrotransposon, Structure, HPC | Present (Aug 05 2024) | |
| LTR_MINER | https://doi.org/10.1186/gb-2004-5-10-r79 | LTR Retrotransposon, Solo-LTR, Filtering, Nested Insertion | ||
| LTR_par | https://www.ncbi.nlm.nih.gov/pubmed/16819780 | LTR Retrotransposon, Structure | ||
| LTR_retriever | https://doi.org/10.1104/pp.17.01310 | LTR Retrotransposon, Structure, Library Generation, Filtering | Present (Aug 05 2024) | |
| LTR_STRUC | https://doi.org/10.1093/bioinformatics/btf878 | LTR Retrotransposon, Structure | Present (Aug 05 2024) | |
| LTR Annotator | https://doi.org/10.17706/ijbbb.2015.5.3.165-174 | LTR Retrotransposon, Library Generation, Annotation | ||
| LTRclassifier | https://doi.org/10.1080/2159256X.2016.1241050 | Link | LTR Retrotransposon, HMM, Classification, Web Server | Present (Aug 05 2024) |
| LtrDetector | https://doi.org/10.1186/s12864-019-5796-9 | De Novo, LTR Retrotransposon, Structure, Annotation, Visualization | Present (Aug 05 2024) | |
| LTRdigest | https://doi.org/10.1093/nar/gkp759 | LTR Retrotransposon, Web Server, Structure, Classification | Present (Aug 05 2024) | |
| LTRharvest | https://doi.org/10.1186/1471-2105-9-18 | Link | LTR Retrotransposon, Structure | Present (Aug 05 2024) |
| LTRphyler | https://doi.org/10.1186/1471-2229-13-172 | LTR Retrotransposon, Classification | Absent (Aug 05 2024) | |
| ltr.pl | https://doi.org/10.1186/1471-2164-8-90 | De Novo, LTR Retrotransposon, HMM | Absent (Aug 05 2024) | |
| LTRpred | https://doi.org/10.21105/joss.02170 | De Novo, Homology, LTR Retrotransposon, Annotation | Present (Aug 05 2024) | |
| LTRsift | https://doi.org/10.1186/1759-8753-3-18 | Link | De Novo, LTR Retrotransposon, Visualization, Library Generation, Annotation | Absent (Aug 05 2024) |
| LTRtype | https://doi.org/10.3389/fpls.2017.00402 | LTR Retrotransposon, Nested Insertion, Homology, | Absent (Aug 05 2024) | |
| Lumpy | https://doi.org/10.1186/gb-2014-15-6-r84 | Structural Variation | Present (Aug 05 2024) | |
| MacSyFinder | https://doi.org/10.1371/journal.pone.0110726 | CRISPR, HMM | Present (Aug 05 2024) | |
| MAGenTA | https://doi.org/10.1093/bioinformatics/btx320 | Web Server, Tn-Seq, Transposon Mutagenesis, NGS/HTS, Visualization, Analysis | Present (Aug 05 2024) | |
| MANTIS | http://doi.org/10.18632/oncotarget.13918 | Simple Sequence Repeat/Microsatellite, Instability, Cancer, NGS/HTS | Present (Aug 05 2024) | |
| MASiVE | https://doi.org/10.1093/bioinformatics/btq454 | LTR Retrotransposon, Sirevirus, Structure, Repeat Extraction | Absent (Aug 05 2024) | |
| McClintock | https://doi.org/10.1534/g3.117.043893 | Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| McClintock2 | https://doi.org/10.1101/2023.02.13.528343 | Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| MCHelper | https://doi.org/10.1101/2023.10.17.562682 | Automated Curation, Classification | Present (Aug 05 2024) | |
| MEGAnE | https://doi.org/10.1101/2022.03.25.485726 | Github | Genotype, Polymorphism, NGS/HTS, Short-Read | Present (Aug 05 2024) |
| MegaLTR | https://doi.org/10.3389/fpls.2023.1237426 | Webserver | LTR Retrotransposon, Detection, Annotation, Webserver, Pipeline | Present (Aug 05 2024) |
| MELT | https://doi.org/10.1101/gr.218032.116 | Genotype, Polymorphism, Illumina, Paired-End, NGS/HTS | Present (Aug 05 2024) | |
| ME-Scan | https://doi.org/10.1186/s13100-020-00207-x | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (Aug 05 2024) | |
| MetaCompare | https://doi.org/10.1093/femsec/fiy079 | NGS/HTS, Metagenomics, AMR/Antibiotic Resistance, BLAST, Pathogen | Present (Aug 05 2024) | |
| MetaPhage | https://doi.org/10.1101/2022.04.17.488583 | NGS/HTS, Metagenomics, Annotation, Classification, Prophage/Bacteriophage | Present (Aug 05 2024) | |
| mer-engine | https://doi.org/10.1101/gr.1350803 | Repeat, De Novo, Library Generation | ||
| mge-cluster | https://doi.org/10.1093/nargab/lqad066 | Gitlab | Plasmid, Classification | Absent (Aug 05 2024) |
| MGERT | https://doi.org/10.1186/s13100-019-0163-6 | Conserved Domain, Repeat Extraction, De Novo, Library Generation, Repeat Extraction | Present (Aug 05 2024) | |
| MGEfinder | https://doi.org/10.1016/j.chom.2019.10.022 | Archaea, Bacteria,, NGS/HTS, Polymorphism, Library Generation | Present (Aug 05 2024) | |
| MGEScan | https://doi.org/10.1093/bioinformatics/btw157 | Web Server, LTR Retrotransposon, LINE/Non-LTR Retrotransposon, HMM | Present (Aug 05 2024) | |
| micRocounter | https://doi.org/10.1534/g3.119.400335 | Simple Sequence Repeat/Microsatellite, Annotation | Present (Aug 05 2024) | |
| MiMSI | https://doi.org/10.1101/2020.09.16.299925 | Simple Sequence Repeat/Microsatellite, Cancer | Present (Aug 05 2024) | |
| MindTheGap | https://doi.org/10.1093/bioinformatics/btu545 | NGS/HTS, Polymorphism, Genotype, K-mer | Present (Aug 05 2024) | |
| MIRU-profiler | https://doi.org/10.7717/peerj.5090 | Tuberculosis, Genotype, Tandem Repeat | Present (Aug 05 2024) | |
| MIRU-VNTRplus | https://doi.org/10.1093/nar/gkq351 | Tuberculosis, Genotype, Tandem Repeat, Web Server | Present (Aug 05 2024) | |
| 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 (Aug 05 2024) | |
| MAK (MITE Analysis Kit) | https://doi.org/10.1093/nar/gkg531 | MITE, Homology, Annotation, ITR/TIR/DNA Transposon | Absent (Aug 05 2024) | |
| MITE Digger | https://doi.org/10.1186/1471-2105-14-186 | MITE, Homology, Annotation, ITR/TIR/DNA Transposon | Absent (Aug 05 2024) | |
| MITE Tracker | https://doi.org/10.1186/s12859-018-2376-y | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Present (Aug 05 2024) | |
| MiteFinder | https://doi.org/10.1109/BIBM.2017.8217644 | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Present (Aug 05 2024) | |
| MiteFinderII | https://doi.org/10.1186/s12920-018-0418-y | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Present (Aug 05 2024) | |
| MITE-Hunter | https://doi.org/10.1093/nar/gkq862 | MITE, Structure, Annotation, ITR/TIR/DNA Transposon | Present (Aug 05 2024) | |
| MJSD | https://doi.org/10.1093/nar/gkp576 | Genomic Island, Nucleotide Composition | ||
| MobileElementFinder | https://doi.org/10.1093/jac/dkaa390 | IS Element, AMR/Antibiotic Resistance, Plasmid, Homology, Web Server | Absent (Aug 05 2024) | |
| MobilomeFINDER | https://doi.org/10.1093/nar/gkm380 | Genomic Island, Microarray, Web Server | Absent (Aug 05 2024) | |
| MOBSTER | https://doi.org/10.1186/s13059-014-0488-x | NGS/HTS, Genotype, Polymorphism, | Present (Aug 05 2024) | |
| ModuleOrganizer | https://doi.org/10.1186/1471-2105-11-474 | Sequence Motif, Visualization, Web Server | ||
| mosaicFlye | https://doi.org/10.1101/2020.01.15.908285 | NGS/HTS, Long-Read, Mosaic Repeat, Segmental Duplication, Assembly | Present (Aug 05 2024) | |
| mreps | https://doi.org/10.1093/nar/gkg617 | Tandem Repeat, De Novo, Library Generation | Present (Aug 05 2024) | |
| MSGIP | https://doi.org/10.1371/journal.pone.0146352 | Genomic Island, Mean Shift Algorithm | Present (Aug 05 2024) | |
| MTGIpick | https://doi.org/10.1093/bib/bbw118 | Genomic Island, K-mer | Present (Aug 05 2024) | |
| msatcommander | https://doi.org/10.1111/j.1471-8286.2007.01884.x | Simple Sequence Repeat/Microsatellite, Primer | Present (Aug 05 2024) | |
| msatfinder | Link | Simple Sequence Repeat/Microsatellite, Primer, Annotation, Repeat Extraction | Present (Aug 05 2024) | |
| mSINGS | https://doi.org/10.1373/clinchem.2014.223677 | Simple Sequence Repeat/Microsatellite, Instability, Polymorphism, Genotype, NGS/HTS, Cancer | Present (Aug 05 2024) | |
| MSIsensor | https://doi.org/10.1093/bioinformatics/btt755 | Simple Sequence Repeat/Microsatellite, Instability, Polymorphism, Genotype, NGS/HTS, Cancer | Present (Aug 05 2024) | |
| 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 (Aug 05 2024) | |
| MyDGR | https://doi.org/10.1093/nar/gkz329 | DGR/Diversity Generating Retroelement, Annotation, BLAST, Alignment, Web Server | Present (Aug 05 2024) | |
| NanoCasTE | https://doi.org/10.1111/jipb.13555 | NGS/HTS, Oxford Nanopore, Cas9, Polymorphism, Genotype | Present (Aug 05 2024) | |
| nanomonsv | https://doi.org/10.1101/2020.07.22.214262 | Structural Variation, NGS/HTS, Long-Read, Cancer | Present (Aug 05 2024) | |
| NanoSatellite | https://doi.org/10.1186/s13059-019-1856-3 | NGS/HTS, Oxford Nanopore, Tandem Repeat | Present (Aug 05 2024) | |
| nanotei | https://doi.org/10.3390/plants10122681 | NGS/HTS, Oxford Nanopore, Polymorphism, Genotype | Present (Aug 05 2024) | |
| NanoTRF | https://doi.org/10.3390/plants11162103 | NGS/HTS, Oxford Nanopore, Tandem Repeat | Present (Aug 05 2024) | |
| NanoVar | https://doi.org/10.1186/s13059-020-01968-7 | NGS/HTS, Oxford Nanopore, Polymorphism, Genotype | Present (Aug 05 2024) | |
| NanoWgsTE | https://doi.org/10.1101/2021.06.11.448052 | Oxford Nanopore, CRISPR, Eukaryotic Transposon | Present (Aug 05 2024) | |
| NCRF | https://doi.org/10.1093/bioinformatics/btz484 | Long-Read, NGS/HTS, Tandem Repeat, De Novo | Present (Aug 05 2024) | |
| ncRNAclassifier | https://doi.org/10.1186/1471-2105-13-246 | ncRNA, miRNA | Absent (Aug 05 2024) | |
| NearTrans | https://doi.org/10.1007/978-3-319-78723-7_32 | Expression, Transcription, Analysis, Pipeline | ||
| nf-repeatmasking | http://doi.org/10.5281/zenodo.1134750 | Repeat Masking, Classification | Present (Aug 05 2024) | |
| NGSEP (Next-Generation Sequencing Experience Platform) | https://doi.org/10.1002/aps3.11520 | Github | NGS/HTS, Homology, Long-Read, Annotation | Present (Aug 05 2024) |
| ngs_te_mapper | https://doi.org/10.1371/journal.pone.0030008 | Target Site Duplication, Homology, NGS/HTS | Present (Aug 05 2024) | |
| NGSEP | https://doi.org/10.1002/aps3.11520 | https://sourceforge.net/projects/ngsep/ | Repeat Masking, Annotation | Present (Aug 05 2024) |
| ntHits | https://doi.org/10.1371/journal.pone.0030008 | K-mer, Repeat | Present (Aug 05 2024) | |
| NTRFinder | https://doi.org/10.1093/nar/gkr1070 | Tandem Repeat | ||
| OASIS | https://doi.org/10.1101/2020.11.02.365809 | IS Element, Homology, Classification | Present (Aug 05 2024) | |
| OMWSA (Optimized Moving Window Spectral Analysis) | https://doi.org/10.1093/bioinformatics/btm008 | Visualization, Repeat | Present (Aug 05 2024) | |
| One_code_to_find_them_all | https://doi.org/10.1186/1759-8753-5-13 | Repeat Extraction, Abundance | Present (Aug 05 2024) | |
| oriTfinder | https://doi.org/10.1093/nar/gky352 | Origin of Transfer, Plasmid, ICE/Integrative and Conjugative Element | Present (Aug 05 2024) | |
| OSTRFPD | https://doi.org/10.1177%2F1176934319843130 | Simple Sequence Repeat/Microsatellite, Alignment, Repeat Extraction, Annotation | Present (Aug 05 2024) | |
| packFinder | https://doi.org/10.1101/2021.06.18.448592 | Link | ITR/TIR/DNA Transposon, MuDR/Mutator, Pack-MULE | Present (Aug 05 2024) |
| PacmonSTR | https://doi.org/10.1093/bioinformatics/btu437 | Tandem Repeat, NGS/HTS, Long-Read, HMM,Homology | Present (Aug 05 2024) | |
| PADLOC (Prokaryotic Antiviral Defence LOCator) | https://doi.org/10.1093/nar/gkac400 | Webserver, Antiviral, Virus | Present (Aug 05 2024) | |
| PAI-IDA | https://doi.org/10.1016/S0378-1097(03)00204-0 | Genomic Island, GC, Codon Usage | ||
| PaliDIS | https://doi.org/10.1099/mgen.0.000917 | IS Element, Metagenomics, Annotation | Present (Aug 05 2024) | |
| panGRP | https://doi.org/10.1093/bioinformatics/btaa792 | Genomic Island | Present (Aug 05 2024) | |
| panISa | https://doi.org/10.1093/bioinformatics/bty479 | De Novo, IS Element, NGS/HTS, Short-Read, Annotation, Homology | Present (Aug 05 2024) | |
| Paragraph | https://doi.org/10.1186/s13059-019-1909-7 | Graph, Structural Variation, Genotype, NGS/HTS, Short-Read | Present (Aug 05 2024) | |
| ParasiTE | https://doi.org/10.1101/2022.09.21.507229 | Long-Read, NGS/HTS, RNA-Seq, Expression, Transcription | Present (Aug 05 2024) | |
| PASTEC | https://doi.org/10.1371/journal.pone.0091929 | Link | Classification | Present (Aug 05 2024) |
| PAtChER | https://doi.org/10.1101/2021.08.25.457666 | ChIP-Seq | Present (Aug 05 2024) | |
| PATIMDB | https://doi.org/10.1002/0471142727.mb1907s86 | Tn-Seq, Transposon Mutagenesis | Absent (Aug 05 2024) | |
| P-Clouds | https://doi.org/10.1016/j.ab.2008.05.015 | De Novo, Library Generation | ||
| PerSVade | https://doi.org/10.1101/2021.11.23.469703 | Structural Variation, Pipeline | Present (Aug 05 2024) | |
| PeSV-Fisher | https://doi.org/10.1371/journal.pone.0063377 | Structural Variation | ||
| PHACTS | https://doi.org/10.1093/bioinformatics/bts014 | Prophage/Bacteriophage, Classification | Present (Aug 05 2024) | |
| PhageAI | https://doi.org/10.1101/2020.07.11.198606 | Prophage/Bacteriophage, Web Server, Machine Learning, Classification | Present (Aug 05 2024) | |
| Phage Commander | https://doi.org/10.1101/2020.11.11.378802 | Prophage/Bacteriophage, Pipeline | Present (Aug 05 2024) | |
| Phage_Finder | https://doi.org/10.1093/nar/gkl732 | Prophage/Bacteriophage, Homology, HMM | Present (Aug 05 2024) | |
| PhaGenus | https://doi.org/10.1093/bib/bbad408 | Prophage/Bacteriophage, Classification | Present (Aug 05 2024) | |
| PhageWeb | https://doi.org/10.3389/fgene.2018.00644 | Prophage/Bacteriophage, Web Server, GC, tRNA | Absent (Aug 05 2024) | |
| PHAST | https://doi.org/10.1093/nar/gkr485 | Prophage/Bacteriophage, Web Server, Homology, Annotation, Visualization | Absent (Aug 05 2024) | |
| PHASTER | https://doi.org/10.1093/nar/gkw387 | Prophage/Bacteriophage, Web Server, Homology, Annotation, Visualization | Present (Aug 05 2024) | |
| Phigaro | https://doi.org/10.1093/bioinformatics/btaa250 | Prophage/Bacteriophage, Annotation | Present (Aug 05 2024) | |
| PhiSpy | https://doi.org/10.1093/nar/gks406 | Prophage/Bacteriophage, Homology | Present (Aug 05 2024) | |
| Phobos | Simple Sequence Repeat/Microsatellite, Library Generation | Present (Aug 05 2024) | ||
| phRAIDER | https://doi.org/10.1093/bioinformatics/btw258 | De Novo,Library Generation | Present (Aug 05 2024) | |
| PhyLTR | LTR Retrotransposon, Annotation, Pipeline, Gene Conversion, Classification, Phylogeny | Present (Aug 05 2024) | ||
| Piano | https://doi.org/10.1186/s12859-014-0419-6 | piRNA, SVM, Classification, Web Server | Absent (Aug 05 2024) | |
| PIATEA | HMM, Annotation Track | Present (Aug 05 2024) | ||
| Pibomd | https://doi.org/10.1039/c4mb00447g | piRNA, SVM | ||
| PILER | https://doi.org/10.1093/bioinformatics/bti1003 | De Novo, Library Generation | Present (Aug 05 2024) | |
| PILFER | https://doi.org/10.1016/j.ygeno.2017.12.005 | piRNA, RNA-Seq, NGS/HTS | Present (Aug 05 2024) | |
| PIMMS (Pragmatic Insertional Mutation Mapping System) | https://doi.org/10.3389/fgene.2015.00139 | NGS/HTS, Tn-Seq | Present (Aug 05 2024) | |
| Pindel | https://doi.org/10.1093/bioinformatics/btp394 | Short-Read, Paired-End, Structural Variation, NGS/HTS | Present (Aug 05 2024) | |
| PingPongPro | https://doi.org/10.1093/bioinformatics/bty578 | piRNA, RNA-Seq, NGS/HTS | Present (Aug 05 2024) | |
| piPipes | https://doi.org/10.1093/bioinformatics/btu647 | piRNA, RNA-Seq, ChIP-Seq, NGS/HTS | Present (Aug 05 2024) | |
| PIPS | https://doi.org/10.1371/journal.pone.0030848 | Genomic Island, Pathogenicity Island, Prediction | Absent (Aug 05 2024) | |
| PiRATE | https://doi.org/10.1186/s12864-018-4763-1 | Web Server, Homology, HMM, Structure, De Novo, Classification, Library Generation, Annotation | Present (Aug 05 2024) | |
| piRNA Pipeline | https://doi.org/10.1093/nar/gky761 | piRNA, NGS/HTS | Present (Aug 05 2024) | |
| piRNN | https://doi.org/10.7717/peerj.5429 | piRNA, K-mer, Convolutional Neural Network | Present (Aug 05 2024) | |
| piRPred | https://doi.org/10.1093/bioinformatics/btu441 | piRNA, SVM | Absent (Aug 05 2024) | |
| piRNAPredictor | https://doi.org/10.1186/s12859-016-1206-3 | piRNA, Prediction | Present (Aug 05 2024) | |
| Plasflow | https://doi.org/10.1093/nar/gkx1321 | Plasmid, Metagenomics, Neural Network | Present (Aug 05 2024) | |
| PlasmidFinder | https://doi.org/10.1128/aac.02412-14 | Plasmid, Homology | Absent (Aug 05 2024) | |
| PlasForest | https://doi.org/10.1186/s12859-021-04270-w | Plasmid, Homology, Classification | Present (Aug 05 2024) | |
| PlasmidHunter | https://doi.org/10.1101/2023.02.01.526640 | Link | Plasmid, Webserver | Present (Aug 05 2024) |
| PlasmidTron | https://doi.org/10.1099/mgen.0.000164 | Plasmid, K-mer | Present (Aug 05 2024) | |
| PlasLR | https://doi.org/10.1101/2021.06.14.448306 | Plasmid, Long-Read | Present (Aug 05 2024) | |
| PlasTrans | https://doi.org/10.1099/mgen.0.000459 | Plasmid | Present (Aug 05 2024) | |
| PlotRep | https://doi.org/10.1093/nar/gkl263 | Dot Plot, Visualization, Repeat Merging | Absent (Aug 05 2024) | |
| 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 (Aug 05 2024) | |
| polymorphicHERV | https://doi.org/10.1371/journal.pcbi.1006564 | ERV/Endogenous Retrovirus, K-mer, Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| PolyMorphPredict | https://doi.org/10.3389/fpls.2018.01966 | Simple Sequence Repeat/Microsatellite, Primer, Web Server | Present (Aug 05 2024) | |
| PoPoolationTE | https://doi.org/10.1093/molbev/msw137 | Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| PostSV | https://doi.org/10.1177/1177932219892957 | Structural Variation, NGS/HTS, SVM | ||
| PPR-Meta | https://doi.org/10.1093/gigascience/giz066 | Link | Prophage/Bacteriophage, Plasmid, Deep Learning | Absent (Aug 05 2024) |
| PRAP | https://doi.org/10.1093/bioinformatics/btt482 | De Novo, Library Generation, Repeat Masking, Archaea, Bacteria | Present (Aug 05 2024) | |
| PredictBias | https://content.iospress.com/articles/in-silico-biology/isb00352 | Genomic Island, Web Server, Homology | Present (Aug 05 2024) | |
| Process_hits | https://doi.org/10.1186/1756-0500-4-482 | Repeat Extraction, Alignment | Present (Aug 05 2024) | |
| ProGeRF | http://doi.org/10.1155/2015/394157 | Simple Sequence Repeat/Microsatellite, Annotation | Absent (Aug 05 2024) | |
| Prophage Finder | https://content.iospress.com/articles/in-silico-biology/isb00235 | Prophage/Bacteriophage, Homology | ||
| ProphET | https://doi.org/10.1371/journal.pone.0223364 | Prophage/Bacteriophage, Homology, Annotation | Present (Aug 05 2024) | |
| Prophinder | https://doi.org/10.1093/bioinformatics/btn043 | Prophage/Bacteriophage, Homology | Absent (Aug 05 2024) | |
| proTRAC | https://doi.org/10.1186/1471-2105-13-5 | piRNA | Absent (Aug 05 2024) | |
| PSSV | https://doi.org/10.1093/bioinformatics/btw605 | Structural Variation, NGS/HTS | Absent (Aug 05 2024) | |
| PTEMD | https://doi.org/10.1093/dnares/dsw011 | Short-Read, NGS/HTS, Genotype, Polymorphism, De Novo | Absent (Aug 05 2024) | |
| Pysim-sv | https://doi.org/10.1186/s12859-017-1464-8 | Structural Variation, NGS/HTS, Simulation | Present (Aug 05 2024) | |
| QDD | https://doi.org/10.1093/bioinformatics/btp670 | Simple Sequence Repeat/Microsatellite, Primer | Absent (Aug 05 2024) | |
| RAIDER | https://doi.org/10.1007/978-3-319-02624-4_16 | De Novo, Repeat, Library Generation | ||
| rampage_alu | https://doi.org/10.1101/gr.249789.119 | RNA-Seq, Expression, Alu, SINE, RAMPAGE, NGS/HTS, Paired-End | Present (Aug 05 2024) | |
| 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 (Aug 05 2024) | |
| RAREFAN (RAyt/REpin Finder and ANalyzer) | https://doi.org/10.24072/pcjournal.244 | Webserver, REPIN/RAYT, Annotation | Present (Aug 05 2024) | |
| RBR | https://doi.org/10.1093/bioinformatics/btl368 | Expression, Transcription, RNA-Seq, Repeat Masking, De Novo | Present (Aug 05 2024) | |
| rCANID | https://doi.org/10.1109/TNB.2019.2908438 | Long-Read, NGS/HTS, Genotype, Polymorphism, Structural Variation | Present (Aug 05 2024) | |
| read2marker | https://doi.org/10.2144/000112025 | Simple Sequence Repeat/Microsatellite, Primer | ||
| REannotate | https://doi.org/10.1186/1471-2164-9-614 | Annotation Parsing, Nested Insertion | Present (Aug 05 2024) | |
| ReAlignerV | https://doi.org/10.1186/1471-2105-9-112 | Alignment | ||
| ReAS | https://doi.org/10.1371/journal.pcbi.0010043 | Email for files: ReAS@genomics.org.cn | De Novo, Library Generation, NGS/HTS | |
| Red | https://doi.org/10.1186/s12859-015-0654-5 | Machine Learning, De Novo, Library Generation | ||
| REdiscoverTE | https://doi.org/10.1038/s41467-019-13035-2 | Expression, Transcription, RNA-Seq | Present (Aug 05 2024) | |
| ReDoSt | https://doi.org/10.1186/1471-2164-12-621 | DIRS, Eukaryotic Retrotransposon, Homology, Structure, Annotation | Absent (Aug 05 2024) | |
| RelocaTE2 | https://doi.org/10.7717/peerj.2942 | Polymorphism, Genotype, NGS/HTS | Present (Aug 05 2024) | |
| RepAHR | https://doi.org/10.1186/s12859-020-03779-w | De Novo, Library Generation, NGS/HTS, K-mer | Present (Aug 05 2024) | |
| RepARK | https://doi.org/10.1093/nar/gku210 | De Novo, Library Generation, NGS/HTS | Present (Aug 05 2024) | |
| RepBox | https://doi.org/10.1186/s12859-023-05419-5 | TE detection, TE annotation, Plants | Present (Aug 05 2024) | |
| REPCLASS | https://uta-ir.tdl.org/uta-ir/handle/10106/455 | Classification | Present (Aug 05 2024) | |
| REPdenovo | https://doi.org/10.1371/journal.pone.0150719 | Short-Read, NGS/HTS, De Novo, Assembly | Present (Aug 05 2024) | |
| RepeatAnalyzer | https://doi.org/10.1186/s12864-016-2686-2 | Simple Sequence Repeat/Microsatellite, Summary, Genotype | Present (Aug 05 2024) | |
| RepeatCraft | https://doi.org/10.1093/bioinformatics/bty745 | Nested Insertion, Visualization | Present (Aug 05 2024) | |
| Repeat Enrichment Estimator | https://doi.org/10.1186/gb-2010-11-6-r69 | NGS/HTS, ChIP-Seq, Repeat, Webserver | Absent (Aug 05 2024) | |
| Repeat Expansion Viewer (REViewer) | Short Read, NGS/HTS, Short Tandem Repeat | Present (Aug 05 2024) | ||
| RepeatExplorer | https://doi.org/10.1093/bioinformatics/btt054 | Link | De Novo, Library Generation, Annotation, NGS/HTS | Present (Aug 05 2024) |
| RepeatFiller | https://doi.org/10.1093/gigascience/giz132 | Genome Alignment, Repeat | Present (Aug 05 2024) | |
| RepeatFinder | https://doi.org/10.1186/gb-2001-2-8-research0027 | Library Generation | Present (Aug 05 2024) | |
| RepeatGluer | https://doi.org/10.1101/gr.2395204 | Repeat Annotation | ||
| RepeatMasker | Repeat Masking, Annotation | Present (Aug 05 2024) | ||
| RepeatModeler | https://doi.org/10.1073/pnas.1921046117 | GitHub | De Novo, Library Generation, Structure, Seed Alignment, Classification | Present (Aug 05 2024) |
| RepeatProfiler | https://doi.org/10.1101/2020.05.22.111252 | NGS/HTS, Short-Read, Visualization, Repeat | Present (Aug 05 2024) | |
| repeatR | Eukaryotic Transposon, RepeatMasker, Annotation, Summary | Present (Aug 05 2024) | ||
| RepeatRunner | https://doi.org/10.1016/j.gene.2006.09.011 | De Novo, Library Generation | Present (Aug 05 2024) | |
| RepeatScout | https://doi.org/10.1093/bioinformatics/bti1018 | De Novo, Library Generation | Absent (Aug 05 2024) | |
| RepeatSeq | https://doi.org/10.1093/nar/gks981 | Simple Sequence Repeat/Microsatellite, Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| RepBox | https://doi.org/10.1186/s12859-023-05419-5 | Detection, Annotation, Classification, Pipeline | Present (Aug 05 2024) | |
| RepEnrich | https://doi.org/10.1186/1471-2164-15-583 | NGS/HTS, RNA-Seq, Expression | Present (Aug 05 2024) | |
| RepEnrich2 | NGS/HTS, RNA-Seq, Expression | Present (Aug 05 2024) | ||
| REPET | https://doi.org/10.1371/journal.pone.0016526 | Link | De Novo, Homology, Structure, Library Generation, Annotation | Present (Aug 05 2024) |
| RepExpress | https://doi.org/10.1002/cpz1.206 | Pipeline, RNA-Seq, Expression | Present (Aug 05 2024) | |
| Repguide | CRISPR, gRNA, Repeat | Present (Aug 05 2024) | ||
| RepLoc | https://doi.org/10.1093/bib/bbaa086 | Repeat, K-mer, Visualization, Annotation, Web Server | Present (Aug 05 2024) | |
| RepLong | https://doi.org/10.1093/bioinformatics/btx717 | De Novo, Long-Read, NGS/HTS | Present (Aug 05 2024) | |
| RepMiner | https://doi.org/10.1101/gr.083360.108 | Repeat, Library Generation, De Novo | Present (Aug 05 2024) | |
| Repseek | https://doi.org/10.1093/bioinformatics/btl519 | Repeat, Library Generation, De Novo | Absent (Aug 05 2024) | |
| RepSeeker | https://ieeexplore.ieee.org/document/5260704 | Repeat, Library Generation, De Novo | ||
| REPuter | https://doi.org/10.1093/nar/29.22.4633 | Repeat, Library Generation, De Novo | Present (Aug 05 2024) | |
| reputils | Github | TE Identification, Alignment, MSA, Manual Curation | Present (Aug 05 2024) | |
| Repsc | Expression, RNA-Seq, Single Cell | Present (Aug 05 2024) | ||
| RetroMap | https://doi.org/10.1186/gb-2004-5-10-r78 | LTR Retrotransposon, Visualization | Present (Aug 05 2024) | |
| retroSeeker | https://doi.org/10.1007/s44307-023-00005-5 | Eukaryotic Retrotransposon, Detection, Homology | Present (Aug 05 2024) | |
| Retroseq | https://doi.org/10.1093/bioinformatics/bts697 | Genotype, Polymorphism, NGS/HTS, Illumina, Paired-End | Present (Aug 05 2024) | |
| RetroSnake | https://doi.org/10.1101/2022.04.08.487607 | NGS/HTS, Endogenous Retrovirus, Annotation | Present (Aug 05 2024) | |
| RetroSom | https://doi.org/10.1101/660779 | Machine Learning, NGS/HTS, Genotype, Polymorphism | Present (Aug 05 2024) | |
| RetroTector | https://doi.org/10.1093/nar/gkm515 | ERV/Endogenous Retrovirus | Present (Aug 05 2024) | |
| retrotransposons-spread | https://doi.org/10.1093/bioinformatics/btw622 | Simulation, LTR Retrotransposon | Present (Aug 05 2024) | |
| 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 (Aug 05 2024) |
| RFPlasmid | https://doi.org/10.1101/2020.07.31.230631 | Link | Plasmid, Resistance, AMR/Antibiotic Resistance, K-mer, Homology | Present (Aug 05 2024) |
| RIPCAL | https://doi.org/10.1186/1471-2105-9-478 | RIP/Repeat-Induced Point Mutation, Mutation, Alignment, Repeat | Present (Aug 05 2024) | |
| RISCI (Repeat Induced Sequence Changes Identifier) | https://doi.org/10.1186/1471-2105-11-609 | NGS/HTS, Genotype, Polymorphism | Present (Aug 05 2024) | |
| RJPrimers | https://doi.org/10.1093/nar/gkq425 | Homology, Primer | Absent (Aug 05 2024) | |
| rMFilter | https://doi.org/10.1093/bioinformatics/btx279 | NGS/HTS, Structural Variation, Long-Read | Present (Aug 05 2024) | |
| rMETL | https://doi.org/10.1093/bioinformatics/btz106 | Long-Read, NGS/HTS, Genotype, Polymorphism | Present (Aug 05 2024) | |
| RNA2DSearch | https://doi.org/10.1261/rna.1264109 | RNA Localization, Prediction, Web Server | Absent (Aug 05 2024) | |
| RPT (Repeat Pattern Toolkit) | Repeat Annotation | |||
| RTAnalyzer | https://doi.org/10.1093/nar/gkm313 | LINE1, LINE/Non-LTR Retrotransposon, Homology | Absent (Aug 05 2024) | |
| RTclass1 | https://doi.org/10.1016/j.gene.2009.07.019 | Classification, LINE/Non-LTR Retrotransposon | Present (Aug 05 2024) | |
| RSPB | https://doi.org/10.1093/molbev/msr282 | MITE, Structure, Library Generation, ITR/TIR/DNA Transposon | Present (Aug 05 2024) | |
| RSVSim | https://doi.org/10.1093/bioinformatics/btt198 | Structural Variation, Simulation | Present (Aug 05 2024) | |
| SalmonTE | https://doi.org/10.1142/9789813235533_0016 | RNA-Seq, Expression, NGS/HTS, Homology | Present (Aug 05 2024) | |
| SAT | https://doi.org/10.1186/1471-2105-8-465 | Simple Sequence Repeat/Microsatellite, Primer, Library Generation, Web Server | Absent (Aug 05 2024) | |
| SatDNA Analyzer | https://doi.org/10.1093/bioinformatics/btm005 | Simple Sequence Repeat/Microsatellite, Alignment, Library Generation | Present (Aug 05 2024) | |
| SATEComp | Link | Homology, Keyword Search, Web Server | Absent (Aug 05 2024) | |
| SciRoKo | https://doi.org/10.1093/bioinformatics/btm157 | Simple Sequence Repeat/Microsatellite, Summary, Annotation | Present (Aug 05 2024) | |
| SCNVSim | https://doi.org/10.1186/s12859-015-0502-7 | CNV/Copy Number Variation, Simulation, Structural Variation | Present (Aug 05 2024) | |
| SCRAMble | https://doi.org/10.1038/s41436-020-0749-x | NGS/HTS, Genotype, Polymorphism, Paired-End | Present (Aug 05 2024) | |
| scTE | https://doi.org/10.1038/s41467-021-21808-x | Single Cell, RNA-Seq, Expression, Eukaryotic Transposon | Present (Aug 05 2024) | |
| SECNVs | https://doi.org/10.3389/fgene.2020.00082 | CNV/Copy Number Variation, Simulation, Expression | Present (Aug 05 2024) | |
| SERpredict | https://doi.org/10.1186/1471-2156-8-78 | RNA-Seq, Expression, Homology | ||
| sideRETRO | https://doi.org/10.1101/2020.03.09.983858 | Pseudogene, CNV/Copy Number Variation, Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| SIGAR | https://doi.org/10.1101/2020.05.05.079426 | NGS/HTS, Short-Read, Split Read | Present (Aug 05 2024) | |
| SIGI-HMM | https://doi.org/10.1186/1471-2105-7-142 | Genomic Island, Codon Usage, HMM | Absent (Aug 05 2024) | |
| Signature.py | https://doi.org/10.1007/978-1-4939-0931-5_12 | Small RNA, piRNA, NGS/HTS | Present (Aug 05 2024) | |
| SimulaTE | https://doi.org/10.1093/bioinformatics/btx772 | Simulation, Genome, NGS/HTS, Genotype, Polymorphism | Present (Aug 05 2024) | |
| SINE-Finder | https://doi.org/10.1105/tpc.111.088682 | SINE, Homology, Motif, Library Generation | Absent (Aug 05 2024) | |
| SINEsFIND | https://doi.org/10.1093/dnares/dsw048 | SINE, Expression, RNA-Seq, NGS/HTS | Present (Aug 05 2024) | |
| SINE_Scan | https://doi.org/10.1093/bioinformatics/btw718 | SINE, Library Generation, Annotation | Present (Aug 05 2024) | |
| SMaRTFinder | Repeat, Annotation | Present (Aug 05 2024) | ||
| SoftSearch | https://doi.org/10.1371/journal.pone.0083356 | Structural Variation, NGS/HTS, Short-Read, Paired-End | ||
| SoftSV | https://doi.org/10.1093/bib/bbv028 | Structural Variation, Paired-End | Present (Aug 05 2024) | |
| SoloTE | https://doi.org/10.1038/s42003-022-04020-5 | RNA-Seq, Expression, Transcription, Single-Cell, NGS/HTS | Present (Aug 05 2024) | |
| sompop | https://doi.org/10.1093/bioinformatics/btaa279 | LINE1, LINE/Non-LTR Retrotransposon, Simulation, Cancer | Present (Aug 05 2024) | |
| somrit | https://www.biorxiv.org/content/10.1101/2023.08.06.552193v2.full.pdf | Retrotransposon, insertion polymorphism, somatic, mosaicism | Present (Aug 05 2024) | |
| SRC (Spark-based RepeatClassifier) | https://doi.org/10.1101/2021.06.03.446998 | RepeatMasker, Classification | Present (Aug 05 2024) | |
| SID (Specific Insertions Detector) | https://doi.org/10.1093/gigascience/gix066 | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (Aug 05 2024) | |
| SPLITREADER | https://doi.org/10.7554/eLife.15716.001 | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (Aug 05 2024) | |
| Sputnik | https://doi.org/10.1038/ng822 | Simple Sequence Repeat/Microsatellite | Absent (Aug 05 2024) | |
| SQUID | https://doi.org/10.1186/s13059-018-1421-5 | RNA-Seq, Expression, NGS/HTS, Structural Variation, Fusion | Present (Aug 05 2024) | |
| SQuIRE | https://doi.org/10.1093/nar/gky1301 | NGS/HTS, RNA-Seq, Expression | Present (Aug 05 2024) | |
| SRF (Satellite Repeat Finder) | https://doi.org/10.1101/gr.278005.123 | Simple Sequence Repeat/Microsatellite, NGS/HTS, Library Generation | Present (Aug 05 2024) | |
| sRNAPipe | https://doi.org/10.1186/s13100-018-0130-7 | Small RNA, RNA-Seq, Annotation | Present (Aug 05 2024) | |
| sRNAplot | https://doi.org/10.1038/s41559-017-0403-4 | Small RNA, piRNA, Visualization | Present (Aug 05 2024) | |
| SRF | https://doi.org/10.1093/bioinformatics/bth103 | Repeat, Web Server | Present (Aug 05 2024) | |
| SSRIT | Simple Sequence Repeat/Microsatellite, Summary | Present (Aug 05 2024) | ||
| SSRfinder | https://doi.org/10.1023/A:1026346121217 | Simple Sequence Repeat/Microsatellite, EST, Expression | ||
| SSR Locator | http://dx.doi.org/10.1155/2008/412696 | Simple Sequence Repeat/Microsatellite, Primer, PCR, Library Generation | Absent (Aug 05 2024) | |
| SSR Primer | https://doi.org/10.1093/bioinformatics/bth104 | Simple Sequence Repeat/Microsatellite, Primer, Library Generation | Absent (Aug 05 2024) | |
| StainedGlass | https://doi.org/10.1093/bioinformatics/btac018 | Link | Simple Sequence Repeat/Microsatellite, Tandem Repeat, Visualization | Present (Aug 05 2024) |
| STAR | https://doi.org/10.1093/bioinformatics/bth335 | Tandem Repeat, Annotation | Present (Aug 05 2024) | |
| starfish | https://doi.org/10.1101/2023.10.24.563810 | Starship, Tyrosine Recombinase, Detection, Annotation | Present (Aug 05 2024) | |
| STEAK | https://doi.org/10.1093/ve/vex023 | NGS/HTS, Genotype, Polymorphism, Annotation | Present (Aug 05 2024) | |
| STRipy | https://doi.org/10.1101/2021.06.13.448220 | Link | Short Tandem Repeat, Genotype, NGS/HTS | Present (Aug 05 2024) |
| STRling | https://doi.org/10.1186/s13059-022-02826-4 | Short Tandem Repeat, Annotation, NGS/HTS | Present (Aug 05 2024) | |
| SURVIVOR | https://doi.org/10.1038/ncomms14061 | Structural Variation, NGS/HTS, Simulation | Present (Aug 05 2024) | |
| SV2 | https://doi.org/10.1093/bioinformatics/btx813 | Structural Variation, Machine Learning, Paired-End | Present (Aug 05 2024) | |
| svaRetro | https://doi.org/10.46471/gigabyte.70 | Structural Variation, Pseudogene, Expression, Transcription, LINE/Non-LTR Retrotransposon | Present (Aug 05 2024) | |
| 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 (Aug 05 2024) | |
| svclassify | https://doi.org/10.1186/s12864-016-2366-2 | Structural Variation, Clustering, Classification | Present (Aug 05 2024) | |
| SVDetect | https://doi.org/10.1093/bioinformatics/btq293 | NGS/HTS, Structural Variation, Paired-End | Present (Aug 05 2024) | |
| SVDSS | NGS/HTS, Structural Variation, Long-Read | Present (Aug 05 2024) | ||
| SVEngine | https://doi.org/10.1093/gigascience/giy081 | Structural Variation, Simulation | Present (Aug 05 2024) | |
| SVelter | https://doi.org/10.1186/s13059-016-0993-1 | Structural Variation, NGS/HTS | Present (Aug 05 2024) | |
| SVIM | https://doi.org/10.1093/bioinformatics/btz041 | NGS/HTS, Long-Read, Structural Variation | Present (Aug 05 2024) | |
| SVM2 | https://doi.org/10.1093/nar/gks606 | Structural Variation, Supervised Learning | ||
| SVmine | https://doi.org/10.1093/bioinformatics/btx455 | Structural Variation, Pipeline | Present (Aug 05 2024) | |
| SVPV | https://doi.org/10.1093/bioinformatics/btx117 | Structural Variation, Visualization | Present (Aug 05 2024) | |
| svviz2 | https://doi.org/10.1093/bioinformatics/btv478 | Structural Variation, Visualization | Present (Aug 05 2024) | |
| SVXplorer | https://doi.org/10.1371/journal.pcbi.1007737 | NGS/HTS, Paired-End, Structural Variation | Present (Aug 05 2024) | |
| SWGIS v2.0 | https://doi.org/10.1186/s12864-018-4724-8 | Genomic Island, Eukaryote, K-mer | Present (Aug 05 2024) | |
| SyRI | https://doi.org/10.1186/s13059-019-1911-0 | Structural Variation, NGS/HTS, Comparative, Whole Genome | Present (Aug 05 2024) | |
| T3E | https://doi.org/10.1186/s13100-022-00285-z | ChIP-Seq, NGS/HTS | Present (Aug 05 2024) | |
| TandemTools | https://doi.org/10.1093/bioinformatics/btaa440 | Tandem Repeat, Long-Read, NGS/HTS, Assembly Polishing, Read Mapping | Present (Aug 05 2024) | |
| Tandem Repeat Annotation Library | https://doi.org/10.1093/bioinformatics/btv306 | Tandem Repeat, Annotation | Present (Aug 05 2024) | |
| Tallymer | https://doi.org/10.1186/1471-2164-9-517 | K-mer Counting | Present (Aug 05 2024) | |
| TANGRAM | https://doi.org/10.1186/1471-2164-15-795 | Polymorphism, Genotype, NGS/HTS | Present (Aug 05 2024) | |
| tantan | https://doi.org/10.1093/nar/gkq1212 | Repeat, Repeat Masking | Absent (Aug 05 2024) | |
| TAPDANCE | https://doi.org/10.1186/1471-2105-13-154 | Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| TAPO | https://doi.org/10.1016/j.febslet.2015.08.025 | Tandem Repeat, Web Server | Present (Aug 05 2024) | |
| TARDIS | http://dx.doi.org/10.1016/j.ymeth.2017.05.030 | Structural Variation, NGS/HTS | Present (Aug 05 2024) | |
| TARGeT (Tree Analysis of Related Genes and Transposons) | https://doi.org/10.1093/nar/gkp295 | Homology, Web Server | Present (Aug 05 2024) | |
| TASR | https://doi.org/10.1093/nar/gkv257 | Small RNA, Annotation | Present (Aug 05 2024) | |
| TCF | https://doi.org/10.1371/journal.pcbi.0030137 | Nested Insertion, Annotation, Web Server | Absent (Aug 05 2024) | |
| TEBreak | https://doi.org/10.1186/s13100-016-0076-6 | Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| TECDetec | https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.718854 | Expression, Transcription, Chimera, NGS/HTS | Present (Aug 05 2024) | |
| TECookbook | https://doi.org/10.1093/nargab/lqad078 | Chip-Seq, NGS/HTS, Analysis | Present (Aug 05 2024) | |
| TE-Aid | https://doi.org/10.1186/s13100-021-00259-7 | Annotation, Classification, Manual Curation, TE Libraries QC | Present (Aug 05 2024) | |
| TE_Density | https://doi.org/10.1186/s13100-022-00264-4 | Annotation, Analysis | Present (Aug 05 2024) | |
| TE Displayer | https://doi.org/10.1093/bioinformatics/btq639 | TE Display | Absent (Aug 05 2024) | |
| TEffectR | https://doi.org/10.7717/peerj.8192 | RNA-Seq, Expression, NGS/HTS, Homology, Annotation | Present (Aug 05 2024) | |
| TE transcripts | https://doi.org/10.1093/bioinformatics/btv422 | Expression, Transcription, RNA-Seq | Present (Aug 05 2024) | |
| TE (Insertion/Deletion Dynamics for Transposable Elements) | https://doi.org/10.1534/genetics.118.301198 | Indel, Insertion Time, LTR Retrotransposon, Aegilops | Present (Aug 05 2024) | |
| TE_Discovery | https://doi.org/10.1101/701888 | Homology, Library Generation, Annotation, Analysis | Present (Aug 05 2024) | |
| TEA | https://doi.org/10.1126/science.1222077 | Genotype, Polymorphism | Present (Aug 05 2024) | |
| TEcandidates | https://doi.org/10.1093/bioinformatics/bty423 | Expression, Transcription, RNA-Seq | Present (Aug 05 2024) | |
| TEclass | https://doi.org/10.1093/bioinformatics/btp084 | Classification | Present (Aug 05 2024) | |
| TEclass2 | https://doi.org/10.1101/2023.10.13.562246 | Classification, Webserver | Present (Aug 05 2024) | |
| Tedna | https://doi.org/10.1093/bioinformatics/btu365 | Assembly, Illumina, Paired-End, NGS/HTS | Present (Aug 05 2024) | |
| TEF (Transposable Element Finder) | https://doi.org/10.1186/s12859-022-05011-3 | Polymorphism, Genotype, NGS/HTS | Present (Aug 05 2024) | |
| TEfinder | https://doi.org/10.3390/genes12020224 | Polymorphism, Genotype, NGS/HTS | Present (Aug 05 2024) | |
| TEFLoN | https://doi.org/10.1093/gbe/evx050 | Annotation, Classification, NGS/HTS, Polymorphism, Genotype, Paired-End, Illumina | Present (Aug 05 2024) | |
| TE-greedy-nester | https://doi.org/10.1093/bioinformatics/btaa632 | Link | Nested Insertion, LTR Retrotransposon | Present (Aug 05 2024) |
| TEGRiP | https://doi.org/10.1101/2021.02.25.432867 | Eukaryotic Transposon, Annotation, Gene | Present (Aug 05 2024) | |
| TE-invasion-simulations | https://doi.org/10.1093/gbe/evy218 | Simulation, Genome, Evolution | Present (Aug 05 2024) | |
| tek2 | https://doi.org/10.1093/molbev/msz220 | Simulation, Genome, Divergence, Evolution | Present (Aug 05 2024) | |
| TE-Learner | https://doi.org/10.1371/journal.pcbi.1006097 | Machine Learning, LTR Retrotransposon, Classification | Absent (Aug 05 2024) | |
| Telescope | https://doi.org/10.1371/journal.pcbi.1006453 | Expression, Transcription, RNA-Seq | Present (Aug 05 2024) | |
| TElocal | Expression, Transcription, RNA-Seq | Present (Aug 05 2024) | ||
| TE-locate | https://doi.org/10.3390/biology1020395 | NGS/HTS, Paired-End, Genotype, Polymorphism | Present (Aug 05 2024) | |
| TELR | NGS/HTS, PacBio, Oxford Nanopore, Long-Read, Genotype, Polymorphism | Present (Aug 05 2024) | ||
| TEmarker | https://doi.org/10.1016/j.xplc.2021.100270 | Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| TEMP | https://doi.org/10.1093/nar/gku323 | Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| TEMP2 | https://doi.org/10.1093/nar/gkab010 | Genotype, Polymorphism, NGS/HTS, Short-Read | Present (Aug 05 2024) | |
| TE-nester | https://ieeexplore.ieee.org/document/8621071 | Structure, Nested Insertion | Present (Aug 05 2024) | |
| 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 (Aug 05 2024) | |
| TEPEAK | https://doi.org/10.1101/2023.10.13.562297 | Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| TEpeaks | ChIP-Seq | Present (Aug 05 2024) | ||
| tephra | Homology, Library Generation, Structure, Classification, Age, Annotation | Present (Aug 05 2024) | ||
| TEPID | https://doi.org/10.7554/eLife.20777.001 | Polymorphism, Genotype, NGS/HTS | Present (Aug 05 2024) | |
| TE-reX | https://doi.org/10.1101/2020.07.02.163816 | Genotype, Polymorphism, Recombination | Present (Aug 05 2024) | |
| TERAD | https://doi.org/10.1111/1755-0998.13080 | RAD-Seq, Repeat Masking, Annotation | Present (Aug 05 2024) | |
| TERL | https://doi.org/10.1093/bib/bbaa185 | Classification, Neural Network | Present (Aug 05 2024) | |
| TESD | https://doi.org/10.1093/bioinformatics/btl454 | Simulation, Genome | Absent (Aug 05 2024) | |
| TESeeker | https://doi.org/10.1186/1471-2105-12-130 | Homology, VirtualBox, Library Generation | Absent (Aug 05 2024) | |
| TEsmall | https://doi.org/10.3389/fgene.2018.00461 | NGS/HTS, Small RNA, piRNA, Annotation | Present (Aug 05 2024) | |
| TEsorter | https://doi.org/10.1093/hr/uhac017 | Link | Classification, HMM | Present (Aug 05 2024) |
| TEspeX | https://doi.org/10.1093/bioinformatics/btac526 | Zenodo | NGS/HTS, Abundance, Expression, Transcription | Present (Aug 05 2024) |
| TE-Tracker | https://doi.org/10.1186/s12859-014-0377-z | Polymorphism, Genotype | Present (Aug 05 2024) | |
| TETyper | https://doi.org/10.1099/mgen.0.000232 | Short-Read, Paired-End, Polymorphism, Genotype, Archaea, Bacteria | Present (Aug 05 2024) | |
| TeXP | https://doi.org/10.1371/journal.pcbi.1007293 | Expression, Transcription, RNA-Seq, NGS/HTS, LINE/Non-LTR Retrotransposon, Activity, Short-Read | Present (Aug 05 2024) | |
| The RIPper | https://doi.org/10.7717/peerj.7447 | Link | RIP/Repeat-Induced Point Mutation, Mutation, GC, Repeat, Web Server | Present (Aug 05 2024) |
| TIDAL | https://doi.org/10.1093/nar/gkv1193 | Genotype, Polymorphism, Illumina, Drosophila | Present (Aug 05 2024) | |
| TIDDIT | https://f1000research.com/articles/6-664/v2 | Rearrangement, NGS/HTS, Structural Variation | Present (Aug 05 2024) | |
| TideHunter | https://doi.org/10.1093/bioinformatics/btz376 | Long-Read, Tandem Repeat, NGS/HTS | Present (Aug 05 2024) | |
| TIDK (Telomere Identifcation toolKit) | Github | De Novo, Telomere, Visualization | Present (Aug 05 2024) | |
| TIGER (Target Integrative Genetic Element Retriever) | https://doi.org/10.1093/nar/gkaa156 | ICE/Integrative and Conjugative Element, Prophage/Bacteriophage | Present (Aug 05 2024) | |
| Tinscan | Comparative, Polymorphism, Genotype | Present (Aug 05 2024) | ||
| TinT (Transposition in Transposition) | https://doi.org/10.1186/1471-2148-10-376 | Nested Insertion, Web Server | Present (Aug 05 2024) | |
| TIF (Transposon Insertion Finder) | https://doi.org/10.1186/1471-2105-15-71 | NGS/HTS, Genotype, Polymorphism, Short-Read | Present (Aug 05 2024) | |
| TIP_finder | https://doi.org/10.3390/biology9090281 | NGS/HTS, Genotype, Polymorphism | Present (Aug 05 2024) | |
| TIPseq-Hunter | https://doi.org/10.1073/pnas.1619797114 | Paired-End, Illumina, Machine Learning | Present (Aug 05 2024) | |
| TIR-Finder | https://doi.org/10.4137/EBO.S10619 | ITR/TIR/DNA Transposon, Web Server, Homology, Structure | Present (Aug 05 2024) | |
| TIR-Learner | https://doi.org/10.1016/j.molp.2019.02.008 | ITR/TIR/DNA Transposon, Homology, Structure, Annotation | Present (Aug 05 2024) | |
| TIRMITE | MITE, HMM, ITR/TIR/DNA Transposon, Annotation | Present (Aug 05 2024) | ||
| T-lex | https://doi.org/10.1093/nar/gkq1291 | Genotype, Polymorphism, NGS/HTS | Absent (Aug 05 2024) | |
| T-lex2 | https://doi.org/10.1093/nar/gku1250 | Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| T-lex3 | https://doi.org/10.1093/bioinformatics/btz727 | Genotype, Polymorphism, NGS/HTS | Present (Aug 05 2024) | |
| TLDR | https://doi.org/10.1101/2020.05.24.113068 | NGS/HTS, Long-Read, Genotype, Polymorphism | ||
| TnComp_finder | Composite Transposon | Absent (Aug 05 2024) | ||
| Tn3_finder | https://doi.org/10.1128/mBio.00452-20 | Transposon | Absent (Aug 05 2024) | |
| Tn3+TA_finder | https://doi.org/10.1128/mBio.00452-20 | Transposon, Toxin-Antitoxin Loci | Present (Aug 05 2024) | |
| Tn-Core | https://doi.org/10.1021/acssynbio.8b00432 | Tn-Seq, Transposon Mutagenesis, RNA-Seq, Metabolic Modelling | Present (Aug 05 2024) | |
| TnPred | http://dx.doi.org/10.1155/2012/678761 | Web Server, Transposase, Archaea, Bacteria, IS Element | Present (Aug 05 2024) | |
| Tn-seq Explorer | https://doi.org/10.1371/journal.pone.0126070 | Tn-Seq, Transposon Mutagenesis | Present (Aug 05 2024) | |
| TRACKPOSON | https://doi.org/10.1038/s41467-018-07974-5 | Genotype, Polymorphism, Paired-End, NGS/HTS | Absent (Aug 05 2024) | |
| TraDIS toolkit | https://doi.org/10.1093/bioinformatics/btw022 | Tn-Seq, Transposon Mutagenesis | Present (Aug 05 2024) | |
| TraFIC | https://doi.org/10.1126/science.1251343 | NGS/HTS, Paired-End, Homo sapiens, Genotype, Polymorphism | Present (Aug 05 2024) | |
| TRANScendence | https://doi.org/10.1186/s12859-017-1824-4 | De Novo, Homology, Structure, Library Generation, Annotation, Web Server | Present (Aug 05 2024) | |
| TRANSIT | https://doi.org/10.1371/journal.pcbi.1004401 | Tn-Seq, Transposon Mutagenesis | Present (Aug 05 2024) | |
| TRANSPO | ITR/TIR/DNA Transposon, Homology | Present (Aug 05 2024) | ||
| TranspoScope | https://doi.org/10.1093/bioinformatics/btaa244 | Genotype, Polymorphism, Visualization, NGS/HTS | Present (Aug 05 2024) | |
| Transposeq | https://doi.org/10.1101/gr.163659.113 | Polymorphism, Genotype, Web Server, Homo sapiens, Eukaryotic Retrotransposon | Absent (Aug 05 2024) | |
| Transposome | https://doi.org/10.1093/bioinformatics/btv059 | De Novo, Assembly, Homology | Present (Aug 05 2024) | |
| Transposon Cluster Finder | https://doi.org/10.1371/journal.pcbi.0030137 | Nested Insertion | Absent (Aug 05 2024) | |
| TransposonPSI | BLAST, Eukaryotic Transposon | Present (Aug 05 2024) | ||
| TransposonUltimate | https://doi.org/10.1093/nar/gkac136 | Link | Eukaryotic Transposon, Library Generation, Classification, Annotation, Structural Variation | Present (Aug 05 2024) |
| TranSurVeyor | https://doi.org/10.1093/nar/gky685 | Genotype, Polymorphism, Paired-End, NGS/HTS | Present (Aug 05 2024) | |
| 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 (Aug 05 2024) | |
| T-REKS | https://doi.org/10.1093/bioinformatics/btp482 | Tandem Repeat | Present (Aug 05 2024) | |
| TRcaller | https://doi.org/10.1101/2023.02.15.528687 | Tandem Repeat, NGS/HTS, Long-Read, Short-Read | Absent (Aug 05 2024) | |
| TrEMOLO | https://doi.org/10.1101/2022.07.21.500944 | NGS/HTS, Long-Read, Oxford Nanopore, Genotype, Polymorphism | Present (Aug 05 2024) | |
| TRF | https://doi.org/10.1093/nar/27.2.573 | Tandem Repeat | Present (Aug 05 2024) | |
| TRGT (Tandem Repeat Genotyping Tool) | https://doi.org/10.1101/2023.05.12.540470 | Tandem Repeat, PacBio, Long-Read, NGS/HTS, Genotype | Present (Aug 05 2024) | |
| TRiCoLOR | https://doi.org/10.1093/gigascience/giaa101 | Tandem Repeat, NGS/HTS, Long-Read | Present (Aug 05 2024) | |
| tRNAscan-SE- On-line | https://doi.org/10.1093/nar/gkw413 | Link | tRNA | Absent (Aug 05 2024) |
| tRNA-DL | https://doi.org/10.1159/000493215 | tRNA, Deep Neural Network | ||
| TROLL | https://doi.org/10.1093/bioinformatics/18.4.634 | Tandem Repeat | Present (Aug 05 2024) | |
| TRTools | https://doi.org/10.1101/2020.03.17.996033 | Tandem Repeat, Genotype | Present (Aug 05 2024) | |
| TrustTEr | https://doi.org/10.1101/2020.07.07.191668 | RNA-Seq, Expression | ||
| TSDFinder | https://doi.org/10.1186/gb-2002-3-10-research0052 | LINE1, LINE/Non-LTR Retrotransposon, Target Site Duplication | Absent (Aug 05 2024) | |
| TypeTE | https://doi.org/10.1093/nar/gkaa074 | Genotype, Polymorphism | Present (Aug 05 2024) | |
| UCSC Repeat Browser | https://doi.org/10.1101/429613 | Repeat, Visualization, Annotation | Present (Aug 05 2024) | |
| ULTRA | https://doi.org/10.1145/3233547.3233604 | Tandem Repeat, HMM, Repeat Masking | Present (Aug 05 2024) | |
| V-ELMpiRNAPred | https://doi.org/10.1142/S0219720016500463 | piRNA, Neural Network | Absent (Aug 05 2024) | |
| VariationHunter | https://doi.org/10.1093/bioinformatics/btq216 | NGS/HTS, Genotype, Polymorphism, Homo sapiens | ||
| VHICA | https://doi.org/10.1093/molbev/msv341 | Horizontal Transfer | Present (Aug 05 2024) | |
| VirSorter | https://doi.org/10.7717/peerj.985 | Prophage/Bacteriophage, Homology, HMM | Present (Aug 05 2024) | |
| VirusSeq | https://doi.org/10.1093/bioinformatics/bts665 | Virus, RNA-Seq, Homo sapiens | Present (Aug 05 2024) | |
| VirusTaxo | https://doi.org/10.1101/2021.04.29.442004 | Virus, K-mer, Classification, Web Server | Present (Aug 05 2024) | |
| VISMapper | https://doi.org/10.1186/s12859-017-1837-z | Virus, NGS/HTS, Web Server, Genotype, Polymorphism, Insertion Site, Visualization | Present (Aug 05 2024) | |
| VisualTE | https://doi.org/10.1186/s12864-015-1351-5 | Annotation, Visualization | ||
| VisualRepbase | https://doi.org/10.1186/1471-2105-9-345 | Annotation, Visualization | Present (Aug 05 2024) | |
| vHULK (Viral Host UnveiLing Kit) | https://doi.org/10.1101/2020.12.06.413476 | Prophage/Bacteriophage | Present (Aug 05 2024) | |
| Vmatch | Repeat Annotation | Present (Aug 05 2024) | ||
| VRprofile | https://doi.org/10.1093/bib/bbw141 | Virulence, AMR/Antibiotic Resistance | Present (Aug 05 2024) | |
| VRprofile2 | https://doi.org/10.1093/nar/gkac321 | Virulence, AMR/Antibiotic Resistance | Present (Aug 05 2024) | |
| WGSSAT | https://doi.org/10.1093/jhered/esx075 | Simple Sequence Repeat/Microsatellite, Repeat Annotation, Primer | Present (Aug 05 2024) | |
| WtP (What the Phage) | https://doi.org/10.1101/2020.07.24.219899 | Prophage/Bacteriophage, Annotation, Classification, Pipeline | Present (Aug 05 2024) | |
| WindowMasker | https://doi.org/10.1093/bioinformatics/bti774 | Repeat Masking, Annotation, De Novo | Absent (Aug 05 2024) | |
| Winnowmap2 | https://doi.org/10.1101/2020.11.01.363887 | Long-Read, NGS/HTS, Repeat | Present (Aug 05 2024) | |
| xenoGI | https://doi.org/10.1186/s12859-018-2038-0 | Genomic Island, Synteny, Phylogeny | Present (Aug 05 2024) | |
| xTea | https://doi.org/10.1038/s41467-021-24041-8 | Eukaryotic Transposon, Polymorphism, Genotype, Long-Read, Short-Read, Pangenome | Present (Aug 05 2024) | |
| YASS | https://doi.org/10.1093/nar/gki478 | Dot Plot, Visualization, Alignment, Web Server | Present (Aug 05 2024) | |
| YORO | https://doi.org/10.1371/journal.pone.0291925 | Classification, LTR Retrotransposon, Convolutional Neural Network | Present (Aug 05 2024) | |
| Zisland Explorer | https://doi.org/10.1093/bib/bbw019 | Genomic Island, GC | Absent (Aug 05 2024) |