| 2lpiRNApred |
https://doi.org/10.1080/15476286.2020.1734382 |
|
piRNA |
| 2-n-way Genome Suite |
https://doi.org/10.1101/gr.262261.120 |
|
Polymorphism, Genotype, Webserver |
| 4-LIN |
https://doi.org/10.1093/sysbio/syac082 |
|
Web Server, Phylogeny, Eukaryotic Retrotransposon |
| AAARF (Assisted Automated Assembler of Repeat Families) |
https://doi.org/10.1186/1471-2105-9-235 |
|
Homology, Alignment |
| AgIn |
https://doi.org/10.1093/bioinformatics/btw360 |
|
PacBio, Methylation |
| AlbaTraDIS |
https://doi.org/10.1371/journal.pcbi.1007980 |
|
Tn-Seq, Transposon Mutagenesis |
| Alien_Hunter |
https://doi.org/10.1093/bioinformatics/btl369 |
|
Genomic Island, HMM |
| alu-detect |
https://doi.org/10.1093/nar/gkt612 |
|
Alu, SINE, Genotype, Polymorphism, NGS/HTS, Paired-End |
| AluMine |
https://doi.org/10.1101/588434 |
|
Alu, SINE, Genotype, Polymorphism, NGS/HTS |
| Alpha-CENTAURI |
https://doi.org/10.1093/bioinformatics/btw101 |
|
Satellite, Centromere, Tandem Repeat, HMM, Long-Read |
| AnnoSINE |
https://doi.org/10.1093/plphys/kiab524 |
|
SINE, Annotation, HMM |
| AnTE |
https://doi.org/10.1371/journal.pgen.1004482 |
|
Simulation, Phylogeny, Bayesian MCMC, Ancestral Reconstruction |
| ANUBIS |
https://doi.org/10.1093/nar/gkaa679 |
|
Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism, Visualization |
| ARTIST |
https://doi.org/10.1371/journal.pgen.1004782 |
|
Tn-Seq, Transposon Mutagenesis, HMM |
| atena |
http://52.71.54.154/packages/devel/bioc/html/atena.html |
|
Pipeline, Expression, Transcription, RNA-Seq |
| 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 |
| Bakta |
https://doi.org/10.1099/mgen.0.000685 |
Link |
Metagenomics, Annotation |
| 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 |
| 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 |
| breseq |
https://doi.org/10.1186/1471-2164-15-1039 |
|
Structural Variation, Polymorphism, Genotype |
| 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 |
| CAFE (Coefficient-based Analysis of Fitness by read Enrichments) |
https://doi.org/10.1093/bioinformatics/btaa1086 |
|
Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism |
| CAULIFINDER |
https://doi.org/10.1186/s13100-022-00288-w |
|
Detection, Annotation, EVE, Plants, Virus |
| CAlu Alu Classifier |
https://doi.org/10.1016/j.cell.2010.05.020 |
|
Genotype, Polymorphism, Homo sapiens, Alu, SINE, Web Server |
| CARP |
https://doi.org/10.1371/journal.pone.0193588 |
|
De Novo, Library Generation, Homology, Annotation |
| CELLO-Seq (single CELl LOng read RNA sequencing) |
https://doi.org/10.1101/2020.10.02.322073 |
|
Single Cell, RNA-Seq, Eukaryotic Transposon |
| Censor |
https://doi.org/10.1016/S0097-8485(96)80013-1 |
|
Annotation, Repeat Masking |
| 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 |
| CIAlign |
https://doi.org/10.7717/peerj.12983 |
|
Alignment, MSA, Manual Curation |
| CLARI-TE |
https://doi.org/10.1186/s13059-014-0546-4 |
|
Homology, Annotation, Nested Insertion |
| ClassifyTE |
https://doi.org/10.1093/bioinformatics/btab146 |
|
Classification, Eukaryotic Transposon |
| CLIFinder |
https://doi.org/10.1093/bioinformatics/btx671 |
|
LINE1, Transcription, RNA-Seq, Expression, Chimera, NGS/HTS |
| CLOVE |
https://doi.org/10.1186/s12859-017-1760-3 |
|
Structural Variation |
| ClustAGE |
https://doi.org/10.1186/s12859-018-2154-x |
|
Comparative, BLAST, Archaea, Bacteria |
| collapse_RepeatMasker_annotation |
https://doi.org/10.1007/978-1-0716-2380-0_21 |
|
Annotation |
| COLOMBO |
https://doi.org/10.1186/1471-2105-7-142 |
|
Genomic Island, Codon Usage, HMM |
| CompTIS |
https://doi.org/10.1128/mSphere.00031-19 |
|
Tn-Seq, Transposon Mutagenesis, PCA |
| CONJscan |
https://doi.org/10.1007/978-1-4939-9877-7_19 |
|
Plasmid, ICE/Integrative and Conjugative Element |
| ConTExt |
https://genome.cshlp.org/content/28/5/714 |
|
Illumina, Paired-End, Homology, NGS/HTS, Polymorphism |
| COSEG |
|
|
Subfamily Identification, Eukaryotic Transposon, Alu, SINE |
| ConsensusSV |
https://doi.org/10.1093/bioinformatics/btac709 |
|
NGS/HTS, Short Read, Illumina, Structural Variation |
| COPLA |
https://doi.org/10.1101/2020.12.15.422809 |
|
Plasmid, Classification, Homology |
| CRISPRCasTyper |
https://doi.org/10.1101/2020.05.15.097824 |
Link |
CRISPR, Classification, Annotation |
| DANTE |
|
Link |
Homology, Library Generation |
| DAWG-PAWS |
https://doi.org/10.1186/1746-4811-5-8 |
|
Homology, HMM, Annotation, Gene Prediction |
| DarkHorse |
https://doi.org/10.1186/gb-2007-8-2-r16 |
|
Horizontal Transfer, Homology, Phylogeny |
| 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 |
| DARTS (Domain-Associated RetroTransposon Search) |
https://doi.org/10.1101/2021.12.03.471067 |
|
Pipeline, Homology, Annotation, Retrotransposon |
| DBSCAN-SWA |
https://doi.org/10.1101/2020.07.12.199018 |
|
Prophage/Bacteriophage, Homology |
| DD-Detection |
https://doi.org/10.1093/bioinformatics/btv621 |
|
NGS/HTS, Illumina, Paired-End, Polymorphism |
| D-Genies |
https://doi.org/10.7717/peerj.4958 |
|
Dot Plot, Visualization |
| DeBreak |
https://doi.org/10.21203/rs.3.rs-1261915/v1 |
|
NGS/HTS, Long-Read, Structural Variation |
| DeepMEI |
https://doi.org/10.1101/2023.03.07.531451 |
|
NGS/HTS, Short Read, Genotype, Polymorphism, Convolutional Neural Network |
| DeepRepeat |
https://doi.org/10.1186/s13059-022-02670-6 |
|
NGS/HTS, Short Tandem Repeat, Long-Read, Oxford Nanopore |
| DeepTE |
https://doi.org/10.1093/bioinformatics/btaa519 |
|
Classification, Convolutional Neural Network |
| Delly |
https://doi.org/10.1093/bioinformatics/bts378 |
|
Structural Variation, NGS/HTS, Short-Read, Paired-End |
| de_novo-identification |
https://doi.org/10.13140/RG.2.2.27068.69765 |
|
De Novo, Eukaryotic Transposon |
| DEPht |
https://doi.org/10.1093/nar/gkac273 |
|
Annotation, Extraction, Prophage/Bacteriophage |
| DeRIP |
https://doi.org/10.1186/1471-2164-11-655 |
|
RIP/Repeat-Induced Point Mutation, Prediction, Fungi |
| 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 |
| detectMITE |
https://doi.org/10.1038/srep19688 |
|
Library Generation, MITE, ITR/TIR/DNA Transposon |
| detettore |
https://doi.org/10.1111/nph.16308 |
|
Polymorphism, Genotype, NGS/HTS, Paired-End |
| DeviaTE |
https://doi.org/10.1111/1755-0998.13030 |
|
NGS/HTS, Abundance, Visualization, Divergence |
| DGRscan |
https://doi.org/10.3390/ijms150814234 |
|
DGR/Diversity Generating Retroelement, Annotation |
| digIS |
https://doi.org/10.1186/s12859-021-04177-6 |
|
IS Element, HMM |
| DiGReF |
https://doi.org/10.1186/1471-2164-13-430 |
|
DGR/Diversity Generating Retroelement, Annotation |
| dimorphicERV |
https://doi.org/10.1186/s13100-018-0142-3 |
|
NGS/HTS, Short-Read, Genotype, Polymorphism, ERV/Endogenous Retrovirus |
| discord-retro |
https://arxiv.org/abs/1501.04268 |
|
Illumina, Paired-End, NGS/HTS, Polymorphism, Genotype |
| DIVE |
https://doi.org/10.1101/2022.06.13.495703 |
|
De Novo, K-mer, Repeat |
| dnaasm |
https://doi.org/10.7490/f1000research.1114626.1 |
|
Repeat, NGS/HTS, De Novo |
| Dna-brnn |
https://doi.org/10.1093/bioinformatics/btz264 |
|
Satellite, Centromere, Neural Network |
| dnaPipeTE |
https://doi.org/10.1093/gbe/evv050 |
GitHub |
NGS/HTS, Assembly, Annotation |
| Domain Organizer |
https://doi.org/10.1093/bioinformatics/btl337 |
|
Alignment, HMM, Domain, Visualization |
| Dotlet |
https://doi.org/10.1093/bioinformatics/16.2.178 |
|
Dot Plot, Visualization |
| dotmatcher |
http://embossgui.sourceforge.net/demo/manual/dotmatcher.html |
|
Dot Plot, Visualization |
| dotplot |
|
|
Dot Plot, Visualization |
| Dotter |
https://doi.org/10.1016/0378-1119(95)00714-8 |
|
Visualization, Dot Plot |
| DTExpress |
https://doi.org/10.1007/978-1-0716-1134-0_2 |
|
RNA-Seq, Expression |
| Duster |
https://peercommunityjournal.org/articles/10.24072/pcjournal.68/ |
|
Library Generation, Homology, K-mer |
| Dysgu |
https://doi.org/10.1093/nar/gkac039 |
|
NGS/HTS, Short-Read, Long-Read, Structural Variation |
| EAHelitron |
https://doi.org/10.1186/s12859-019-2945-8 |
|
Helitron, Structure |
| EarlGrey |
https://doi.org/10.21203/rs.3.rs-1812599/v1 |
|
Pipeline, Annotation, Repeat Masking, Homology, De Novo, Library Generation |
| Easymap |
https://doi.org/10.3389/fpls.2021.655286 |
Link |
Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism |
| Ecc_finder |
https://www.frontiersin.org/articles/10.3389/fpls.2021.743742/abstract |
|
essDNA, NGS/HTS, Oxford Nanopore |
| ECCsplorer |
https://doi.org/10.1186/s12859-021-04545-2 |
|
eccDNA, Identification, Active TEs |
| EDTA |
https://doi.org/10.1186/s13059-019-1905-y |
|
Library Generation, Filtering, Structure, De Novo |
| EGID |
https://doi.org/10.6026/007/97320630007311 |
|
Genomic Island, Prediction |
| ELAN |
https://doi.org/10.1093/nar/gkr337 |
|
Homology, Insertion Site, Consensus |
| ELITE (Efficiently Locating Insertions of Transposable Elements) |
https://doi.org/10.1145/3307339.3342182 |
|
Genotype, Polymorphism, NGS/HTS |
| EpiTEome |
https://doi.org/10.1186/s13059-017-1232-0 |
|
Polymorphism, Genotype, NGS/HTS, Methyl-Seq, Bisulfite, Methylation, |
| ERVcaller |
https://doi.org/10.1093/bioinformatics/btz205 |
|
ERV/Endogenous Retrovirus, Homo sapiens, NGS/HTS, Polymorphism, Genotype |
| ERVmap |
https://doi.org/10.1073/pnas.1814589115 |
|
ERV/Endogenous Retrovirus, RNA-Seq, Transcriptome,Homo sapiens |
| ESAP Plus |
https://doi.org/10.1186/s12864-016-3328-4 |
|
Simple Sequence Repeat/Microsatellite, Expression, EST, Clustering, Repeat Masking |
| ESMP |
https://doi.org/10.6026/97320630008206 |
|
Simple Sequence Repeat/Microsatellite, Expression, EST, Clustering |
| ESSENTIALS |
https://doi.org/10.1371/journal.pone.0043012 |
|
Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism |
| ExoPLOT |
https://doi.org/10.1016/j.ygeno.2022.110434 |
|
RNA-Seq, Expression, Transcription, NGS/HTS |
| ExpansionHunter |
https://doi.org/10.1101/gr.225672.117 |
|
Short Read, NGS/HTS, Short Tandem Repeat |
| ExpansionHunter Denovo |
https://doi.org/10.1101/863035 |
|
Short-Read, NGS/HTS, Short Tandem Repeat |
| ExplorATE |
https://doi.org/10.1093/bioinformatics/btac354 |
|
Expression, Transcription, RNA-Seq |
| FasTE |
https://doi.org/10.1111/1755-0998.13489 |
|
De Novo, Homology, Library Generation, Annotation, Pipeline, Classification |
| Fastq2LoxDel |
https://doi.org/10.1101/2020.07.14.202044 |
|
Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism |
| FASTQINS |
https://doi.org/10.1093/nar/gkaa679 |
|
Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism, Read Mapping |
| FindTelomeres |
|
|
Telomere |
| FiTnEss (Finding Tn-Seq Essentials) |
https://doi.org/10.1073/pnas.1900570116 |
|
Tn-Seq, Transposon Mutagenesis, NGS/HTS, Polymorphism |
| FlexDotPlot |
https://doi.org/10.1101/2020.04.03.023655 |
|
Visualization, Dot Plot |
| FlexiDot |
https://doi.org/10.1093/bioinformatics/bty395 |
|
Visualization, Dot Plot |
| FORRepeats |
https://doi.org/10.1093/bioinformatics/btf843 |
|
Repeat, Detection |
| FullSSR |
https://doi.org/10.1155/2016/6040124 |
|
Simple Sequence Repeat/Microsatellite, Primer |
| GASVPro |
https://doi.org/10.1186/gb-2012-13-3-r22 |
|
Structural Variation, NGS/HTS,Paired-End |
| GC-Profile |
https://doi.org/10.2174/1389202915999140328163125 |
|
Genomic Island, GC |
| GeIST |
https://doi.org/10.1093/bioinformatics/btv350 |
|
Tn-Seq, Transposon Mutagenesis |
| Generic Repeat Finder |
https://doi.org/10.1104/pp.19.00386 |
|
LTR Retrotransposon, MITE, Inverted Repeat, ITR/TIR/DNA Transposon |
| GeneTEFlow |
https://doi.org/10.1101/2020.04.28.065862 |
|
RNA-Seq, NGS/HTS, Nextflow |
| geNomad |
https://doi.org/10.1038/s41587-023-01953-y |
|
Virus, Plasmid, Machine Learning, Detection, Classification |
| Genome ARTIST v2 |
https://doi.org/10.3390/ijms232012686 |
|
Tn-Seq, Transposon Mutagenesis, Drosophila, ITR/TIR/DNA Transposon |
| GenomeDiff |
|
|
Dot Plot, Visualization, Virus |
| GenomeTools |
https://doi.ieeecomputersociety.org/10.1109/TCBB.2013.68 |
|
Genome Annotation |
| Gepard |
https://doi.org/10.1093/bioinformatics/btm039 |
|
Visualization, Dot Plot |
| G-IMEx |
https://doi.org/10.6026/97320630005221 |
|
Simple Sequence Repeat/Microsatellite, Repeat Extraction, Annotation |
| GI-Cluster |
https://doi.org/10.1142/S0219720018400103 |
|
Genomic Island, GC, Codon Usage, K-mer |
| GIDetector |
https://doi.org/10.1186/1471-2164-11-S2-S1 |
|
Genomic Island, Pipeline |
| GIHunter |
https://doi.org/10.4172/jpb.1000322 |
|
Genomic Island, Prediction |
| GI-POP |
https://doi.org/10.1016/j.gene.2012.11.063 |
|
Genomic Island, SVM, Annotation |
| GIPSy |
https://doi.org/10.1016/j.jbiotec.2015.09.008 |
|
Genomic Island, GC, Homology, HMM |
| GIST |
https://doi.org/10.6026/97320630008203 |
|
Genomic Island, Pipeline |
| GI-SVM |
https://doi.org/10.1142/S0219720016400035 |
|
Genomic Island, SVM, K-mer |
| GIV |
https://doi.org/10.6026/97320630009879 |
|
Genomic Island, Visualization |
| GMATA |
https://doi.org/10.3389/fpls.2016.01350 |
|
Simple Sequence Repeat/Microsatellite, Repeat Extraction, Annotation, Primer |
| GMATo |
https://doi.org/10.6026/97320630009541 |
|
Simple Sequence Repeat/Microsatellite, Repeat Annotation |
| GPAC (Genome Presence/Absence Compiler) |
https://doi.org/10.1093/molbev/msu276 |
|
Polymorphism, Genotype |
| GraffiTE |
https://doi.org/10.1101/2023.09.11.557209 |
|
Polymorphism, Structural Variation, Long-Read, NGS/HTS, Assemblies, Pangenomes, Graph-Genome, Genotype |
| GraphTyper |
https://doi.org/10.1038/ng.3964 |
|
Structural Variation, Short-Read, NGS/HTS |
| GraphTyper2 |
https://doi.org/10.1038/s41467-019-13341-9 |
|
Structural Variation, Short-Read, NGS/HTS |
| GRASPER |
https://doi.org/10.1089/cmb.2013.0129 |
|
Structural Variation, Repeat, Homology, NGS/HTS, Paired-End |
| GREAM |
https://doi.org/10.1371/journal.pone.0133647 |
|
Mammal, Web Server,Genome, Analysis |
| Greedier |
https://doi.org/10.1093/bioinformatics/btm613 |
|
Homology, Repeat Masking,Nested Insertion, Graph |
| HashRepeatFinder |
https://doi.org/10.1007/s12539-015-0119-6 |
|
De Novo, Library Generation |
| HDRSM (Highly Divergent Repeat Search Method) |
https://doi.org/10.1186/s12859-021-03977-0 |
|
SINE |
| HelitronFinder |
https://doi.org/10.1186/1471-2164-9-51 |
|
Helitron, Structure |
| HelitronScanner |
https://doi.org/10.1073/pnas.1410068111 |
|
Helitron, Structure |
| HelSearch |
https://doi.org/10.1073/pnas.0905563106 |
|
Helitron, Structure |
| 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 |
| HiTE |
https://doi.org/10.1101/2023.05.23.541879 |
|
Detection, Annotation |
| HiTea |
https://doi.org/10.1101/2020.04.27.060145 |
|
Hi-C, NGS/HTS, Genotype, Polymorphism |
| HIVIntact |
https://doi.org/10.1186/s12977-021-00561-5 |
|
Retrovirus, Activity |
| HMMER |
https://doi.org/10.1371/journal.pcbi.1000069 |
|
HMM |
| HomologMiner |
https://doi.org/10.1093/bioinformatics/btm048 |
|
Homology, Genome, Comparative |
| HTdetect |
https://doi.org/10.1093/gbe/evu026 |
|
Horizontal Transfer, Homology |
| ICEfinder |
https://doi.org/10.1093/nar/gky1123 |
Link |
ICE/Integrative and Conjugative Element, HMM |
| ICEscreen |
https://doi.org/10.1093/nargab/lqac079 |
|
ICE/Integrative and Conjugative Element, HMM |
| IDSSR |
https://doi.org/10.3390/ijms20143497 |
|
Simple Sequence Repeat/Microsatellite, NGS/HTS, Paired-End, Primer, Repeat Annotation, Polymorphism |
| IGIPT |
https://doi.org/10.6026/007/97320630007307 |
|
Genomic Island, Nucleotide Composition, Visualization |
| iMapper |
https://doi.org/10.1093/bioinformatics/btn541 |
|
Genome, Ensembl, Transposon Mutagenesis |
| IMEx |
https://doi.org/10.1093/bioinformatics/btm097 |
|
Simple Sequence Repeat/Microsatellite, Annotation, Web Server |
| iMGEins |
https://doi.org/10.1186/s12864-018-5290-9 |
|
NGS/HTS, Paired-End, Homology, Genotype, Polymorphism, Annotation |
| iMSAT |
https://doi.org/10.1186/1471-2164-15-858 |
|
Simple Sequence Repeat/Microsatellite, Illumina, NGS/HTS, Short-Read, Genotype, Polymorphism, Repeat Extraction |
| 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 |
| InFire |
https://doi.org/10.1093/bioinformatics/btr672 |
|
Transposon Mutagenesis, Web Server,Restriction Digestion |
| InMut-Finder |
https://doi.org/10.1186/s12864-021-08206-9 |
|
NGS/HTS, Onxford Nanopore, Tn-Seq, Transposon Mutagenesis |
| Inpactor |
https://doi.org/10.3390/biology7020032 |
|
LTR Retrotransposon, Classification, Insertion Time |
| Inpactor2 |
https://doi.org/10.1093/bib/bbac511 |
|
LTR Retrotransposon, Classification, Insertion Time, Neural Network |
| InsertionMapper |
https://doi.org/10.1186/1471-2164-14-679 |
|
Tn-Seq, Transposon Mutagenesis, NGS/HTS |
| In-seq/Tn-seq |
http://doi.org/10.1038/nprot.2011.417 |
|
Tn-Seq, Transposon Mutagenesis |
| INSurVeyor |
https://doi.org/10.1038/s41467-023-38870-2 |
|
Polymorphism, Short-Reads, NGS/HTS, Paired-End |
| IntegronFinder |
https://doi.org/10.1093/nar/gkw319 |
Link |
Integron, HMM |
| IntegronFinder 2.0 |
https://doi.org/10.3390/microorganisms10040700 |
|
Integron, HMM |
| Invade |
https://doi.org/10.1093/molbev/msz079 |
|
Simulation, piRNA, Genome |
| IpiRId |
https://doi.org/10.1371/journal.pone.0179787 |
|
piRNA, SVM |
| IRescue |
https://doi.org/10.1101/2022.09.16.508229 |
|
Single-Cell, NGS/HTS, RNA-Seq, Expression, Transcription |
| 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 |
| ISAbR_finder |
|
|
IS Element, AMR/Antibiotic Resistance |
| ISCompare |
https://doi.org/10.1093/g3journal/jkab181 |
|
IS Element, Genotype, Polymorphism |
| IScan |
https://doi.org/10.1093/nar/gkm597 |
|
IS Element, Homology |
| ISEScan |
https://doi.org/10.1093/bioinformatics/btx433 |
|
IS Element, HMM, Homology, Library Generation |
| IslandCafe |
https://doi.org/10.1534/g3.119.400562 |
|
Genomic Island |
| IslandPath-DIMOB |
https://doi.org/10.1093/bioinformatics/bty095 |
|
Genomic Island, HMM, Homology, K-mer |
| IslandPick |
https://doi.org/10.1186/1471-2105-9-329 |
|
Genomic Island, Homology, Comparative |
| IslandViewer 4 |
https://doi.org/10.1093/bioinformatics/btp030 |
|
Genomic Island, Visualization, Web Server |
| ISMapper |
https://doi.org/10.1186/s12864-015-1860-2 |
|
IS Element, Short-Read, NGS/HTS, Illumina, Paired-End, Polymorphism, Genotype |
| ISQuest |
https://doi.org/10.1093/bioinformatics/btv388 |
|
IS Element, NGS/HTS, Homology |
| ISsaga |
https://doi.org/10.1186/gb-2011-12-3-r30 |
|
Homology, Annotation, IS Element |
| ISseeker |
https://doi.org/10.1099/mgen.0.000062 |
|
IS Element, Homology, Comparative |
| iSVP |
https://doi.org/10.1186/1752-0509-7-s6-s8 |
|
Structural Variation, Pipeline |
| ITIS (Identification of Transposon Insertion Sites) |
https://doi.org/10.1186/s12859-015-0507-2 |
|
Genotype, Polymorphism, NGS/HTS |
| IUPACpal |
https://doi.org/10.1186/s12859-021-03983-2 |
|
Inverted Repeat |
| JDotter |
https://doi.org/10.1093/bioinformatics/btg406 |
|
Dot Plot, Visualization |
| Jitterbug |
https://doi.org/10.1186/s12864-015-1975-5 |
|
Paired-End, NGS/HTS, Polymorphism, Genotype, |
| KKSC Significance Test |
https://doi.org/10.1371/journal.pcbi.1004812 |
|
Polymorphism, Genotype, LINE/Non-LTR Retrotransposon, Age, Speciation |
| L1EM |
https://doi.org/10.1093/bioinformatics/btz724 |
|
Expression, Transcription, LINE1, LINE/Non-LTR Retrotransposon, Activity, NGS/HTS |
| L1PD (LINE-1 Pattern Detection) |
https://doi.org/10.1186/s12859-022-04907-4 |
|
LINE1, LINE/Non-LTR Retrotransposon, K-mer |
| L1Seq |
https://doi.org/10.1101/gr.106419.110 |
|
LINE/Non-LTR Retrotransposon, LINE1 |
| LAST |
https://doi.org/10.1186/s13059-015-0670-9 |
|
Alignment, Repeat |
| LIONS |
https://doi.org/10.1093/bioinformatics/btz130 |
|
RNA-Seq, Transcription |
| LocaTR |
https://doi.org/10.1186/s12864-016-3043-1 |
|
LTR Retrotransposon, Homology, Structure, Annotation |
| LocusMasterTE |
https://doi.org/10.1101/2023.03.21.533716 |
|
NGS/HTS, Long-Read, Expression, Transcription, RNA-Seq |
| LongRepMarker |
https://doi.org/10.1093/nar/gkab563 |
|
De Novo, K-mer, Library Generation, Long-Read, Short-Read |
| Look4LTRs |
https://doi.org/10.1101/2023.07.28.551030 |
|
LTR Retrotransposon, Nested Insertion, Annotation |
| LoRTE |
https://doi.org/10.1186/s13100-017-0088-x |
|
Long-Read, PacBio, NGS/HTS, Genotype, Polymorphism, Indel,Homology |
| LoRTIS-SS |
https://doi.org/10.1101/2022.05.26.493556 |
|
Long-Read, NGS/HTS, Oxford Nanopore, Tn-Seq, Transposon Mutagenesis |
| LTR_FINDER |
https://doi.org/10.1093/nar/gkm286 |
|
LTR Retrotransposon, Structure, Web Server |
| LTR_FINDER_parallel |
https://doi.org/10.1186/s13100-019-0193-0 |
|
LTR Retrotransposon, Structure, HPC |
| 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 |
| LTR_STRUC |
https://doi.org/10.1093/bioinformatics/btf878 |
|
LTR Retrotransposon, Structure |
| 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 |
| LtrDetector |
https://doi.org/10.1186/s12864-019-5796-9 |
|
De Novo, LTR Retrotransposon, Structure, Annotation, Visualization |
| LTRdigest |
https://doi.org/10.1093/nar/gkp759 |
|
LTR Retrotransposon, Web Server, Structure, Classification |
| LTRharvest |
https://doi.org/10.1186/1471-2105-9-18 |
Link |
LTR Retrotransposon, Structure |
| LTRphyler |
https://doi.org/10.1186/1471-2229-13-172 |
|
LTR Retrotransposon, Classification |
| ltr.pl |
https://doi.org/10.1186/1471-2164-8-90 |
|
De Novo, LTR Retrotransposon, HMM |
| LTRpred |
https://doi.org/10.21105/joss.02170 |
|
De Novo, Homology, LTR Retrotransposon, Annotation |
| LTRsift |
https://doi.org/10.1186/1759-8753-3-18 |
Link |
De Novo, LTR Retrotransposon, Visualization, Library Generation, Annotation |
| LTRtype |
https://doi.org/10.3389/fpls.2017.00402 |
|
LTR Retrotransposon, Nested Insertion, Homology, |
| Lumpy |
https://doi.org/10.1186/gb-2014-15-6-r84 |
|
Structural Variation |
| MacSyFinder |
https://doi.org/10.1371/journal.pone.0110726 |
|
CRISPR, HMM |
| MAGenTA |
https://doi.org/10.1093/bioinformatics/btx320 |
|
Web Server, Tn-Seq, Transposon Mutagenesis, NGS/HTS, Visualization, Analysis |
| MANTIS |
http://doi.org/10.18632/oncotarget.13918 |
|
Simple Sequence Repeat/Microsatellite, Instability, Cancer, NGS/HTS |
| MASiVE |
https://doi.org/10.1093/bioinformatics/btq454 |
|
LTR Retrotransposon, Sirevirus, Structure, Repeat Extraction |
| McClintock |
https://doi.org/10.1534/g3.117.043893 |
|
Genotype, Polymorphism, NGS/HTS |
| McClintock2 |
https://doi.org/10.1101/2023.02.13.528343 |
|
Genotype, Polymorphism, NGS/HTS |
| MCHelper |
https://doi.org/10.1101/2023.10.17.562682 |
|
Automated Curation, Classification |
| MEGAnE |
https://doi.org/10.1101/2022.03.25.485726 |
Github |
Genotype, Polymorphism, NGS/HTS, Short-Read |
| MegaLTR |
https://doi.org/10.3389/fpls.2023.1237426 |
Webserver |
LTR Retrotransposon, Detection, Annotation, Webserver, Pipeline |
| MELT |
https://doi.org/10.1101/gr.218032.116 |
|
Genotype, Polymorphism, Illumina, Paired-End, NGS/HTS |
| ME-Scan |
https://doi.org/10.1186/s13100-020-00207-x |
|
Genotype, Polymorphism, Paired-End, NGS/HTS |
| MetaCompare |
https://doi.org/10.1093/femsec/fiy079 |
|
NGS/HTS, Metagenomics, AMR/Antibiotic Resistance, BLAST, Pathogen |
| MetaPhage |
https://doi.org/10.1101/2022.04.17.488583 |
|
NGS/HTS, Metagenomics, Annotation, Classification, Prophage/Bacteriophage |
| 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 |
| MGERT |
https://doi.org/10.1186/s13100-019-0163-6 |
|
Conserved Domain, Repeat Extraction, De Novo, Library Generation, Repeat Extraction |
| MGEfinder |
https://doi.org/10.1016/j.chom.2019.10.022 |
|
Archaea, Bacteria,, NGS/HTS, Polymorphism, Library Generation |
| MGEScan |
https://doi.org/10.1093/bioinformatics/btw157 |
|
Web Server, LTR Retrotransposon, LINE/Non-LTR Retrotransposon, HMM |
| micRocounter |
https://doi.org/10.1534/g3.119.400335 |
|
Simple Sequence Repeat/Microsatellite, Annotation |
| MiMSI |
https://doi.org/10.1101/2020.09.16.299925 |
|
Simple Sequence Repeat/Microsatellite, Cancer |
| MindTheGap |
https://doi.org/10.1093/bioinformatics/btu545 |
|
NGS/HTS, Polymorphism, Genotype, K-mer |
| MIRU-profiler |
https://doi.org/10.7717/peerj.5090 |
|
Tuberculosis, Genotype, Tandem Repeat |
| MIRU-VNTRplus |
https://doi.org/10.1093/nar/gkq351 |
|
Tuberculosis, Genotype, Tandem Repeat, Web Server |
| 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 |
| MAK (MITE Analysis Kit) |
https://doi.org/10.1093/nar/gkg531 |
|
MITE, Homology, Annotation, ITR/TIR/DNA Transposon |
| MITE Digger |
https://doi.org/10.1186/1471-2105-14-186 |
|
MITE, Homology, Annotation, ITR/TIR/DNA Transposon |
| MITE Tracker |
https://doi.org/10.1186/s12859-018-2376-y |
|
MITE, Structure, Library Generation, ITR/TIR/DNA Transposon |
| MiteFinder |
https://doi.org/10.1109/BIBM.2017.8217644 |
|
MITE, Structure, Library Generation, ITR/TIR/DNA Transposon |
| MiteFinderII |
https://doi.org/10.1186/s12920-018-0418-y |
|
MITE, Structure, Library Generation, ITR/TIR/DNA Transposon |
| MITE-Hunter |
https://doi.org/10.1093/nar/gkq862 |
|
MITE, Structure, Annotation, ITR/TIR/DNA Transposon |
| 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 |
| MobilomeFINDER |
https://doi.org/10.1093/nar/gkm380 |
|
Genomic Island, Microarray, Web Server |
| MOBSTER |
https://doi.org/10.1186/s13059-014-0488-x |
|
NGS/HTS, Genotype, Polymorphism, |
| 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 |
| mreps |
https://doi.org/10.1093/nar/gkg617 |
|
Tandem Repeat, De Novo, Library Generation |
| MSGIP |
https://doi.org/10.1371/journal.pone.0146352 |
|
Genomic Island, Mean Shift Algorithm |
| MTGIpick |
https://doi.org/10.1093/bib/bbw118 |
|
Genomic Island, K-mer |
| msatcommander |
https://doi.org/10.1111/j.1471-8286.2007.01884.x |
|
Simple Sequence Repeat/Microsatellite, Primer |
| msatfinder |
Link |
|
Simple Sequence Repeat/Microsatellite, Primer, Annotation, Repeat Extraction |
| mSINGS |
https://doi.org/10.1373/clinchem.2014.223677 |
|
Simple Sequence Repeat/Microsatellite, Instability, Polymorphism, Genotype, NGS/HTS, Cancer |
| MSIsensor |
https://doi.org/10.1093/bioinformatics/btt755 |
|
Simple Sequence Repeat/Microsatellite, Instability, Polymorphism, Genotype, NGS/HTS, Cancer |
| 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 |
| MyDGR |
https://doi.org/10.1093/nar/gkz329 |
|
DGR/Diversity Generating Retroelement, Annotation, BLAST, Alignment, Web Server |
| NanoCasTE |
https://doi.org/10.1111/jipb.13555 |
|
NGS/HTS, Oxford Nanopore, Cas9, Polymorphism, Genotype |
| nanomonsv |
https://doi.org/10.1101/2020.07.22.214262 |
|
Structural Variation, NGS/HTS, Long-Read, Cancer |
| NanoSatellite |
https://doi.org/10.1186/s13059-019-1856-3 |
|
NGS/HTS, Oxford Nanopore, Tandem Repeat |
| nanotei |
https://doi.org/10.3390/plants10122681 |
|
NGS/HTS, Oxford Nanopore, Polymorphism, Genotype |
| NanoTRF |
https://doi.org/10.3390/plants11162103 |
|
NGS/HTS, Oxford Nanopore, Tandem Repeat |
| NanoVar |
https://doi.org/10.1186/s13059-020-01968-7 |
|
NGS/HTS, Oxford Nanopore, Polymorphism, Genotype |
| NanoWgsTE |
https://doi.org/10.1101/2021.06.11.448052 |
|
Oxford Nanopore, CRISPR, Eukaryotic Transposon |
| NCRF |
https://doi.org/10.1093/bioinformatics/btz484 |
|
Long-Read, NGS/HTS, Tandem Repeat, De Novo |
| ncRNAclassifier |
https://doi.org/10.1186/1471-2105-13-246 |
|
ncRNA, miRNA |
| 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 |
| NGSEP (Next-Generation Sequencing Experience Platform) |
https://doi.org/10.1002/aps3.11520 |
Github |
NGS/HTS, Homology, Long-Read, Annotation |
| ngs_te_mapper |
https://doi.org/10.1371/journal.pone.0030008 |
|
Target Site Duplication, Homology, NGS/HTS |
| NGSEP |
https://doi.org/10.1002/aps3.11520 |
https://sourceforge.net/projects/ngsep/ |
Repeat Masking, Annotation |
| ntHits |
https://doi.org/10.1371/journal.pone.0030008 |
|
K-mer, Repeat |
| NTRFinder |
https://doi.org/10.1093/nar/gkr1070 |
|
Tandem Repeat |
| OASIS |
https://doi.org/10.1101/2020.11.02.365809 |
|
IS Element, Homology, Classification |
| OMWSA (Optimized Moving Window Spectral Analysis) |
https://doi.org/10.1093/bioinformatics/btm008 |
|
Visualization, Repeat |
| One_code_to_find_them_all |
https://doi.org/10.1186/1759-8753-5-13 |
|
Repeat Extraction, Abundance |
| oriTfinder |
https://doi.org/10.1093/nar/gky352 |
|
Origin of Transfer, Plasmid, ICE/Integrative and Conjugative Element |
| OSTRFPD |
https://doi.org/10.1177%2F1176934319843130 |
|
Simple Sequence Repeat/Microsatellite, Alignment, Repeat Extraction, Annotation |
| packFinder |
https://doi.org/10.1101/2021.06.18.448592 |
Link |
ITR/TIR/DNA Transposon, MuDR/Mutator, Pack-MULE |
| PacmonSTR |
https://doi.org/10.1093/bioinformatics/btu437 |
|
Tandem Repeat, NGS/HTS, Long-Read, HMM,Homology |
| PADLOC (Prokaryotic Antiviral Defence LOCator) |
https://doi.org/10.1093/nar/gkac400 |
|
Webserver, Antiviral, Virus |
| 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 |
| panGRP |
https://doi.org/10.1093/bioinformatics/btaa792 |
|
Genomic Island |
| panISa |
https://doi.org/10.1093/bioinformatics/bty479 |
|
De Novo, IS Element, NGS/HTS, Short-Read, Annotation, Homology |
| Paragraph |
https://doi.org/10.1186/s13059-019-1909-7 |
|
Graph, Structural Variation, Genotype, NGS/HTS, Short-Read |
| ParasiTE |
https://doi.org/10.1101/2022.09.21.507229 |
|
Long-Read, NGS/HTS, RNA-Seq, Expression, Transcription |
| PASTEC |
https://doi.org/10.1371/journal.pone.0091929 |
|
Classification |
| PAtChER |
https://doi.org/10.1101/2021.08.25.457666 |
|
ChIP-Seq |
| PATIMDB |
https://doi.org/10.1002/0471142727.mb1907s86 |
|
Tn-Seq, Transposon Mutagenesis |
| 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 |
| PeSV-Fisher |
https://doi.org/10.1371/journal.pone.0063377 |
|
Structural Variation |
| PHACTS |
https://doi.org/10.1093/bioinformatics/bts014 |
|
Prophage/Bacteriophage, Classification |
| PhageAI |
https://doi.org/10.1101/2020.07.11.198606 |
|
Prophage/Bacteriophage, Web Server, Machine Learning, Classification |
| Phage Commander |
https://doi.org/10.1101/2020.11.11.378802 |
|
Prophage/Bacteriophage, Pipeline |
| Phage_Finder |
https://doi.org/10.1093/nar/gkl732 |
|
Prophage/Bacteriophage, Homology, HMM |
| PhaGenus |
https://doi.org/10.1093/bib/bbad408 |
|
Prophage/Bacteriophage, Classification |
| PhageWeb |
https://doi.org/10.3389/fgene.2018.00644 |
|
Prophage/Bacteriophage, Web Server, GC, tRNA |
| PHAST |
https://doi.org/10.1093/nar/gkr485 |
|
Prophage/Bacteriophage, Web Server, Homology, Annotation, Visualization |
| PHASTER |
https://doi.org/10.1093/nar/gkw387 |
|
Prophage/Bacteriophage, Web Server, Homology, Annotation, Visualization |
| Phigaro |
https://doi.org/10.1093/bioinformatics/btaa250 |
|
Prophage/Bacteriophage, Annotation |
| PhiSpy |
https://doi.org/10.1093/nar/gks406 |
|
Prophage/Bacteriophage, Homology |
| Phobos |
|
|
Simple Sequence Repeat/Microsatellite, Library Generation |
| phRAIDER |
https://doi.org/10.1093/bioinformatics/btw258 |
|
De Novo,Library Generation |
| PhyLTR |
|
|
LTR Retrotransposon, Annotation, Pipeline, Gene Conversion, Classification, Phylogeny |
| Piano |
https://doi.org/10.1186/s12859-014-0419-6 |
|
piRNA, SVM, Classification, Web Server |
| PIATEA |
|
|
HMM, Annotation Track |
| Pibomd |
https://doi.org/10.1039/c4mb00447g |
|
piRNA, SVM |
| PILER |
https://doi.org/10.1093/bioinformatics/bti1003 |
|
De Novo, Library Generation |
| PILFER |
https://doi.org/10.1016/j.ygeno.2017.12.005 |
|
piRNA, RNA-Seq, NGS/HTS |
| PIMMS (Pragmatic Insertional Mutation Mapping System) |
https://doi.org/10.3389/fgene.2015.00139 |
|
NGS/HTS, Tn-Seq |
| Pindel |
https://doi.org/10.1093/bioinformatics/btp394 |
|
Short-Read, Paired-End, Structural Variation, NGS/HTS |
| PingPongPro |
https://doi.org/10.1093/bioinformatics/bty578 |
|
piRNA, RNA-Seq, NGS/HTS |
| piPipes |
https://doi.org/10.1093/bioinformatics/btu647 |
|
piRNA, RNA-Seq, ChIP-Seq, NGS/HTS |
| PIPS |
https://doi.org/10.1371/journal.pone.0030848 |
|
Genomic Island, Pathogenicity Island, Prediction |
| PiRATE |
https://doi.org/10.1186/s12864-018-4763-1 |
|
Web Server, Homology, HMM, Structure, De Novo, Classification, Library Generation, Annotation |
| piRNA Pipeline |
https://doi.org/10.1093/nar/gky761 |
|
piRNA, NGS/HTS |
| piRNN |
https://doi.org/10.7717/peerj.5429 |
|
piRNA, K-mer, Convolutional Neural Network |
| piRPred |
https://doi.org/10.1093/bioinformatics/btu441 |
|
piRNA, SVM |
| piRNAPredictor |
https://doi.org/10.1186/s12859-016-1206-3 |
|
piRNA, Prediction |
| Plasflow |
https://doi.org/10.1093/nar/gkx1321 |
|
Plasmid, Metagenomics, Neural Network |
| PlasmidFinder |
https://doi.org/10.1128/aac.02412-14 |
|
Plasmid, Homology |
| PlasForest |
https://doi.org/10.1186/s12859-021-04270-w |
|
Plasmid, Homology, Classification |
| PlasmidHunter |
https://doi.org/10.1101/2023.02.01.526640 |
Link |
Plasmid, Webserver |
| PlasmidTron |
https://doi.org/10.1099/mgen.0.000164 |
|
Plasmid, K-mer |
| PlasLR |
https://doi.org/10.1101/2021.06.14.448306 |
|
Plasmid, Long-Read |
| PlasTrans |
https://doi.org/10.1099/mgen.0.000459 |
|
Plasmid |
| PlotRep |
https://doi.org/10.1093/nar/gkl263 |
|
Dot Plot, Visualization, Repeat Merging |
| 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 |
| polymorphicHERV |
https://doi.org/10.1371/journal.pcbi.1006564 |
|
ERV/Endogenous Retrovirus, K-mer, Genotype, Polymorphism, NGS/HTS |
| PolyMorphPredict |
https://doi.org/10.3389/fpls.2018.01966 |
|
Simple Sequence Repeat/Microsatellite, Primer, Web Server |
| PoPoolationTE |
https://doi.org/10.1093/molbev/msw137 |
|
Genotype, Polymorphism, NGS/HTS |
| 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 |
| PRAP |
https://doi.org/10.1093/bioinformatics/btt482 |
|
De Novo, Library Generation, Repeat Masking, Archaea, Bacteria |
| PredictBias |
https://content.iospress.com/articles/in-silico-biology/isb00352 |
|
Genomic Island, Web Server, Homology |
| Process_hits |
https://doi.org/10.1186/1756-0500-4-482 |
|
Repeat Extraction, Alignment |
| ProGeRF |
http://doi.org/10.1155/2015/394157 |
|
Simple Sequence Repeat/Microsatellite, Annotation |
| 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 |
| Prophinder |
https://doi.org/10.1093/bioinformatics/btn043 |
|
Prophage/Bacteriophage, Homology |
| proTRAC |
https://doi.org/10.1186/1471-2105-13-5 |
|
piRNA |
| PSSV |
https://doi.org/10.1093/bioinformatics/btw605 |
|
Structural Variation, NGS/HTS |
| PTEMD |
https://doi.org/10.1093/dnares/dsw011 |
|
Short-Read, NGS/HTS, Genotype, Polymorphism, De Novo |
| Pysim-sv |
https://doi.org/10.1186/s12859-017-1464-8 |
|
Structural Variation, NGS/HTS, Simulation |
| QDD |
https://doi.org/10.1093/bioinformatics/btp670 |
|
Simple Sequence Repeat/Microsatellite, Primer |
| 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 |
| 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 |
| RAREFAN (RAyt/REpin Finder and ANalyzer) |
https://doi.org/10.24072/pcjournal.244 |
|
Webserver, REPIN/RAYT, Annotation |
| RBR |
https://doi.org/10.1093/bioinformatics/btl368 |
|
Expression, Transcription, RNA-Seq, Repeat Masking, De Novo |
| rCANID |
https://doi.org/10.1109/TNB.2019.2908438 |
|
Long-Read, NGS/HTS, Genotype, Polymorphism, Structural Variation |
| 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 |
| 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 |
| ReDoSt |
https://doi.org/10.1186/1471-2164-12-621 |
|
DIRS, Eukaryotic Retrotransposon, Homology, Structure, Annotation |
| RelocaTE2 |
https://doi.org/10.7717/peerj.2942 |
|
Polymorphism, Genotype, NGS/HTS |
| RepAHR |
https://doi.org/10.1186/s12859-020-03779-w |
|
De Novo, Library Generation, NGS/HTS, K-mer |
| RepARK |
https://doi.org/10.1093/nar/gku210 |
|
De Novo, Library Generation, NGS/HTS |
| RepBox |
https://doi.org/10.1186/s12859-023-05419-5 |
|
TE detection, TE annotation, Plants |
| REPCLASS |
https://uta-ir.tdl.org/uta-ir/handle/10106/455 |
|
Classification |
| REPdenovo |
https://doi.org/10.1371/journal.pone.0150719 |
|
Short-Read, NGS/HTS, De Novo, Assembly |
| RepeatAnalyzer |
https://doi.org/10.1186/s12864-016-2686-2 |
|
Simple Sequence Repeat/Microsatellite, Summary, Genotype |
| RepeatCraft |
https://doi.org/10.1093/bioinformatics/bty745 |
|
Nested Insertion, Visualization |
| Repeat Enrichment Estimator |
https://doi.org/10.1186/gb-2010-11-6-r69 |
|
NGS/HTS, ChIP-Seq, Repeat, Webserver |
| Repeat Expansion Viewer (REViewer) |
|
|
Short Read, NGS/HTS, Short Tandem Repeat |
| RepeatExplorer |
https://doi.org/10.1093/bioinformatics/btt054 |
Link |
De Novo, Library Generation, Annotation, NGS/HTS |
| RepeatFiller |
https://doi.org/10.1093/gigascience/giz132 |
|
Genome Alignment, Repeat |
| RepeatFinder |
https://doi.org/10.1186/gb-2001-2-8-research0027 |
|
Library Generation |
| RepeatGluer |
https://doi.org/10.1101/gr.2395204 |
|
Repeat Annotation |
| RepeatMasker |
|
|
Repeat Masking, Annotation |
| RepeatModeler |
https://doi.org/10.1073/pnas.1921046117 |
GitHub |
De Novo, Library Generation, Structure, Seed Alignment, Classification |
| RepeatProfiler |
https://doi.org/10.1101/2020.05.22.111252 |
|
NGS/HTS, Short-Read, Visualization, Repeat |
| repeatR |
|
|
Eukaryotic Transposon, RepeatMasker, Annotation, Summary |
| RepeatRunner |
https://doi.org/10.1016/j.gene.2006.09.011 |
|
De Novo, Library Generation |
| RepeatScout |
https://doi.org/10.1093/bioinformatics/bti1018 |
|
De Novo, Library Generation |
| RepeatSeq |
https://doi.org/10.1093/nar/gks981 |
|
Simple Sequence Repeat/Microsatellite, Genotype, Polymorphism, NGS/HTS |
| RepBox |
https://doi.org/10.1186/s12859-023-05419-5 |
|
Detection, Annotation, Classification, Pipeline |
| RepEnrich |
https://doi.org/10.1186/1471-2164-15-583 |
|
NGS/HTS, RNA-Seq, Expression |
| RepEnrich2 |
|
|
NGS/HTS, RNA-Seq, Expression |
| REPET |
https://doi.org/10.1371/journal.pone.0016526 |
Link |
De Novo, Homology, Structure, Library Generation, Annotation |
| RepExpress |
https://doi.org/10.1002/cpz1.206 |
|
Pipeline, RNA-Seq, Expression |
| Repguide |
|
|
CRISPR, gRNA, Repeat |
| RepLoc |
https://doi.org/10.1093/bib/bbaa086 |
|
Repeat, K-mer, Visualization, Annotation, Web Server |
| RepLong |
https://doi.org/10.1093/bioinformatics/btx717 |
|
De Novo, Long-Read, NGS/HTS |
| RepMiner |
https://doi.org/10.1101/gr.083360.108 |
|
Repeat, Library Generation, De Novo |
| Repseek |
https://doi.org/10.1093/bioinformatics/btl519 |
|
Repeat, Library Generation, De Novo |
| 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 |
| reputils |
|
Github |
TE Identification, Alignment, MSA, Manual Curation |
| Repsc |
|
|
Expression, RNA-Seq, Single Cell |
| RetroMap |
https://doi.org/10.1186/gb-2004-5-10-r78 |
|
LTR Retrotransposon, Visualization |
| retroSeeker |
https://doi.org/10.1007/s44307-023-00005-5 |
|
Eukaryotic Retrotransposon, Detection, Homology |
| Retroseq |
https://doi.org/10.1093/bioinformatics/bts697 |
|
Genotype, Polymorphism, NGS/HTS, Illumina, Paired-End |
| RetroSnake |
https://doi.org/10.1101/2022.04.08.487607 |
|
NGS/HTS, Endogenous Retrovirus, Annotation |
| RetroSom |
https://doi.org/10.1101/660779 |
|
Machine Learning, NGS/HTS, Genotype, Polymorphism |
| RetroTector |
https://doi.org/10.1093/nar/gkm515 |
|
ERV/Endogenous Retrovirus |
| retrotransposons-spread |
https://doi.org/10.1093/bioinformatics/btw622 |
|
Simulation, LTR Retrotransposon |
| 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 |
| RFPlasmid |
https://doi.org/10.1101/2020.07.31.230631 |
Link |
Plasmid, Resistance, AMR/Antibiotic Resistance, K-mer, Homology |
| RIPCAL |
https://doi.org/10.1186/1471-2105-9-478 |
|
RIP/Repeat-Induced Point Mutation, Mutation, Alignment, Repeat |
| RISCI (Repeat Induced Sequence Changes Identifier) |
https://doi.org/10.1186/1471-2105-11-609 |
|
NGS/HTS, Genotype, Polymorphism |
| RJPrimers |
https://doi.org/10.1093/nar/gkq425 |
|
Homology, Primer |
| rMFilter |
https://doi.org/10.1093/bioinformatics/btx279 |
|
NGS/HTS, Structural Variation, Long-Read |
| rMETL |
https://doi.org/10.1093/bioinformatics/btz106 |
|
Long-Read, NGS/HTS, Genotype, Polymorphism |
| RNA2DSearch |
https://doi.org/10.1261/rna.1264109 |
|
RNA Localization, Prediction, Web Server |
| RPT (Repeat Pattern Toolkit) |
|
|
Repeat Annotation |
| RTAnalyzer |
https://doi.org/10.1093/nar/gkm313 |
|
LINE1, LINE/Non-LTR Retrotransposon, Homology |
| RTclass1 |
https://doi.org/10.1016/j.gene.2009.07.019 |
|
Classification, LINE/Non-LTR Retrotransposon |
| RSPB |
https://doi.org/10.1093/molbev/msr282 |
|
MITE, Structure, Library Generation, ITR/TIR/DNA Transposon |
| RSVSim |
https://doi.org/10.1093/bioinformatics/btt198 |
|
Structural Variation, Simulation |
| SalmonTE |
https://doi.org/10.1142/9789813235533_0016 |
|
RNA-Seq, Expression, NGS/HTS, Homology |
| SAT |
https://doi.org/10.1186/1471-2105-8-465 |
|
Simple Sequence Repeat/Microsatellite, Primer, Library Generation, Web Server |
| SatDNA Analyzer |
https://doi.org/10.1093/bioinformatics/btm005 |
|
Simple Sequence Repeat/Microsatellite, Alignment, Library Generation |
| SATEComp |
Link |
|
Homology, Keyword Search, Web Server |
| SciRoKo |
https://doi.org/10.1093/bioinformatics/btm157 |
|
Simple Sequence Repeat/Microsatellite, Summary, Annotation |
| SCNVSim |
https://doi.org/10.1186/s12859-015-0502-7 |
|
CNV/Copy Number Variation, Simulation, Structural Variation |
| SCRAMble |
https://doi.org/10.1038/s41436-020-0749-x |
|
NGS/HTS, Genotype, Polymorphism, Paired-End |
| scTE |
https://doi.org/10.1038/s41467-021-21808-x |
|
Single Cell, RNA-Seq, Expression, Eukaryotic Transposon |
| SECNVs |
https://doi.org/10.3389/fgene.2020.00082 |
|
CNV/Copy Number Variation, Simulation, Expression |
| 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 |
| SIGAR |
https://doi.org/10.1101/2020.05.05.079426 |
|
NGS/HTS, Short-Read, Split Read |
| SIGI-HMM |
https://doi.org/10.1186/1471-2105-7-142 |
|
Genomic Island, Codon Usage, HMM |
| Signature.py |
https://doi.org/10.1007/978-1-4939-0931-5_12 |
|
Small RNA, piRNA, NGS/HTS |
| SimulaTE |
https://doi.org/10.1093/bioinformatics/btx772 |
|
Simulation, Genome, NGS/HTS, Genotype, Polymorphism |
| SINE-Finder |
https://doi.org/10.1105/tpc.111.088682 |
|
SINE, Homology, Motif, Library Generation |
| SINEsFIND |
https://doi.org/10.1093/dnares/dsw048 |
|
SINE, Expression, RNA-Seq, NGS/HTS |
| SINE_Scan |
https://doi.org/10.1093/bioinformatics/btw718 |
|
SINE, Library Generation, Annotation |
| SMaRTFinder |
|
|
Repeat, Annotation |
| 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 |
| SoloTE |
https://doi.org/10.1038/s42003-022-04020-5 |
|
RNA-Seq, Expression, Transcription, Single-Cell, NGS/HTS |
| sompop |
https://doi.org/10.1093/bioinformatics/btaa279 |
|
LINE1, LINE/Non-LTR Retrotransposon, Simulation, Cancer |
| somrit |
https://www.biorxiv.org/content/10.1101/2023.08.06.552193v2.full.pdf |
|
Retrotransposon, insertion polymorphism, somatic, mosaicism |
| SRC (Spark-based RepeatClassifier) |
https://doi.org/10.1101/2021.06.03.446998 |
|
RepeatMasker, Classification |
| SID (Specific Insertions Detector) |
https://doi.org/10.1093/gigascience/gix066 |
|
Genotype, Polymorphism, Paired-End, NGS/HTS |
| SPLITREADER |
https://doi.org/10.7554/eLife.15716.001 |
|
Genotype, Polymorphism, Paired-End, NGS/HTS |
| Sputnik |
https://doi.org/10.1038/ng822 |
|
Simple Sequence Repeat/Microsatellite |
| SQUID |
https://doi.org/10.1186/s13059-018-1421-5 |
|
RNA-Seq, Expression, NGS/HTS, Structural Variation, Fusion |
| SQuIRE |
https://doi.org/10.1093/nar/gky1301 |
|
NGS/HTS, RNA-Seq, Expression |
| SRF (Satellite Repeat Finder) |
https://doi.org/10.1101/gr.278005.123 |
|
Simple Sequence Repeat/Microsatellite, NGS/HTS, Library Generation |
| sRNAPipe |
https://doi.org/10.1186/s13100-018-0130-7 |
|
Small RNA, RNA-Seq, Annotation |
| sRNAplot |
https://doi.org/10.1038/s41559-017-0403-4 |
|
Small RNA, piRNA, Visualization |
| SRF |
https://doi.org/10.1093/bioinformatics/bth103 |
|
Repeat, Web Server |
| SSRIT |
|
|
Simple Sequence Repeat/Microsatellite, Summary |
| 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 |
| SSR Primer |
https://doi.org/10.1093/bioinformatics/bth104 |
|
Simple Sequence Repeat/Microsatellite, Primer, Library Generation |
| StainedGlass |
https://doi.org/10.1093/bioinformatics/btac018 |
Link |
Simple Sequence Repeat/Microsatellite, Tandem Repeat, Visualization |
| STAR |
https://doi.org/10.1093/bioinformatics/bth335 |
|
Tandem Repeat, Annotation |
| starfish |
https://doi.org/10.1101/2023.10.24.563810 |
|
Starship/Tyroson, Tyrosine Recombinase, Detection, Annotation |
| STEAK |
https://doi.org/10.1093/ve/vex023 |
|
NGS/HTS, Genotype, Polymorphism, Annotation |
| STRipy |
https://doi.org/10.1101/2021.06.13.448220 |
Link |
Short Tandem Repeat, Genotype, NGS/HTS |
| STRling |
https://doi.org/10.1186/s13059-022-02826-4 |
|
Short Tandem Repeat, Annotation, NGS/HTS |
| SURVIVOR |
https://doi.org/10.1038/ncomms14061 |
|
Structural Variation, NGS/HTS, Simulation |
| SV2 |
https://doi.org/10.1093/bioinformatics/btx813 |
|
Structural Variation, Machine Learning, Paired-End |
| svaRetro |
https://doi.org/10.46471/gigabyte.70 |
|
Structural Variation, Pseudogene, Expression, Transcription, LINE/Non-LTR Retrotransposon |
| 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 |
| svclassify |
https://doi.org/10.1186/s12864-016-2366-2 |
|
Structural Variation, Clustering, Classification |
| SVDetect |
https://doi.org/10.1093/bioinformatics/btq293 |
|
NGS/HTS, Structural Variation, Paired-End |
| SVDSS |
|
|
NGS/HTS, Structural Variation, Long-Read |
| SVEngine |
https://doi.org/10.1093/gigascience/giy081 |
|
Structural Variation, Simulation |
| SVelter |
https://doi.org/10.1186/s13059-016-0993-1 |
|
Structural Variation, NGS/HTS |
| SVIM |
https://doi.org/10.1093/bioinformatics/btz041 |
|
NGS/HTS, Long-Read, Structural Variation |
| SVM2 |
https://doi.org/10.1093/nar/gks606 |
|
Structural Variation, Supervised Learning |
| SVmine |
https://doi.org/10.1093/bioinformatics/btx455 |
|
Structural Variation, Pipeline |
| SVPV |
https://doi.org/10.1093/bioinformatics/btx117 |
|
Structural Variation, Visualization |
| svviz2 |
https://doi.org/10.1093/bioinformatics/btv478 |
|
Structural Variation, Visualization |
| SVXplorer |
https://doi.org/10.1371/journal.pcbi.1007737 |
|
NGS/HTS, Paired-End, Structural Variation |
| SWGIS v2.0 |
https://doi.org/10.1186/s12864-018-4724-8 |
|
Genomic Island, Eukaryote, K-mer |
| SyRI |
https://doi.org/10.1186/s13059-019-1911-0 |
|
Structural Variation, NGS/HTS, Comparative, Whole Genome |
| T3E |
https://doi.org/10.1186/s13100-022-00285-z |
|
ChIP-Seq, NGS/HTS |
| TandemTools |
https://doi.org/10.1093/bioinformatics/btaa440 |
|
Tandem Repeat, Long-Read, NGS/HTS, Assembly Polishing, Read Mapping |
| Tandem Repeat Annotation Library |
https://doi.org/10.1093/bioinformatics/btv306 |
|
Tandem Repeat, Annotation |
| Tallymer |
https://doi.org/10.1186/1471-2164-9-517 |
|
K-mer Counting |
| TANGRAM |
https://doi.org/10.1186/1471-2164-15-795 |
|
Polymorphism, Genotype, NGS/HTS |
| tantan |
https://doi.org/10.1093/nar/gkq1212 |
|
Repeat, Repeat Masking |
| TAPDANCE |
https://doi.org/10.1186/1471-2105-13-154 |
|
Genotype, Polymorphism, NGS/HTS |
| TAPO |
https://doi.org/10.1016/j.febslet.2015.08.025 |
|
Tandem Repeat, Web Server |
| TARDIS |
http://dx.doi.org/10.1016/j.ymeth.2017.05.030 |
|
Structural Variation, NGS/HTS |
| TARGeT (Tree Analysis of Related Genes and Transposons) |
https://doi.org/10.1093/nar/gkp295 |
|
Homology, Web Server |
| TASR |
https://doi.org/10.1093/nar/gkv257 |
|
Small RNA, Annotation |
| TCF |
https://doi.org/10.1371/journal.pcbi.0030137 |
|
Nested Insertion, Annotation, Web Server |
| TEBreak |
https://doi.org/10.1186/s13100-016-0076-6 |
|
Genotype, Polymorphism, NGS/HTS |
| TECDetec |
https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.718854 |
|
Expression, Transcription, Chimera, NGS/HTS |
| TECookbook |
https://doi.org/10.1093/nargab/lqad078 |
|
Chip-Seq, NGS/HTS, Analysis |
| TE-Aid |
https://doi.org/10.1186/s13100-021-00259-7 |
|
Annotation, Classification, Manual Curation, TE Libraries QC |
| TE_Density |
https://doi.org/10.1186/s13100-022-00264-4 |
|
Annotation, Analysis |
| TE Displayer |
https://doi.org/10.1093/bioinformatics/btq639 |
|
TE Display |
| TEffectR |
https://doi.org/10.7717/peerj.8192 |
|
RNA-Seq, Expression, NGS/HTS, Homology, Annotation |
| TE transcripts |
https://doi.org/10.1093/bioinformatics/btv422 |
|
Expression, Transcription, RNA-Seq |
| TE (Insertion/Deletion Dynamics for Transposable Elements) |
https://doi.org/10.1534/genetics.118.301198 |
|
Indel, Insertion Time, LTR Retrotransposon, Aegilops |
| TE_Discovery |
https://doi.org/10.1101/701888 |
|
Homology, Library Generation, Annotation, Analysis |
| TEA |
https://doi.org/10.1126/science.1222077 |
|
Genotype, Polymorphism |
| TEcandidates |
https://doi.org/10.1093/bioinformatics/bty423 |
|
Expression, Transcription, RNA-Seq |
| TEclass |
https://doi.org/10.1093/bioinformatics/btp084 |
|
Classification |
| TEclass2 |
https://doi.org/10.1101/2023.10.13.562246 |
|
Classification, Webserver |
| Tedna |
https://doi.org/10.1093/bioinformatics/btu365 |
|
Assembly, Illumina, Paired-End, NGS/HTS |
| TEF (Transposable Element Finder) |
https://doi.org/10.1186/s12859-022-05011-3 |
|
Polymorphism, Genotype, NGS/HTS |
| TEfinder |
https://doi.org/10.3390/genes12020224 |
|
Polymorphism, Genotype, NGS/HTS |
| TEFLoN |
https://doi.org/10.1093/gbe/evx050 |
|
Annotation, Classification, NGS/HTS, Polymorphism, Genotype, Paired-End, Illumina |
| TE-greedy-nester |
https://doi.org/10.1093/bioinformatics/btaa632 |
Link |
Nested Insertion, LTR Retrotransposon |
| TEGRiP |
https://doi.org/10.1101/2021.02.25.432867 |
|
Eukaryotic Transposon, Annotation, Gene |
| TE-invasion-simulations |
https://doi.org/10.1093/gbe/evy218 |
|
Simulation, Genome, Evolution |
| tek2 |
https://doi.org/10.1093/molbev/msz220 |
|
Simulation, Genome, Divergence, Evolution |
| TE-Learner |
https://doi.org/10.1371/journal.pcbi.1006097 |
|
Machine Learning, LTR Retrotransposon, Classification |
| Telescope |
https://doi.org/10.1371/journal.pcbi.1006453 |
|
Expression, Transcription, RNA-Seq |
| TElocal |
|
|
Expression, Transcription, RNA-Seq |
| TE-locate |
https://doi.org/10.3390/biology1020395 |
|
NGS/HTS, Paired-End, Genotype, Polymorphism |
| TELR |
|
|
NGS/HTS, PacBio, Oxford Nanopore, Long-Read, Genotype, Polymorphism |
| TEmarker |
https://doi.org/10.1016/j.xplc.2021.100270 |
|
Genotype, Polymorphism, NGS/HTS |
| TEMP |
https://doi.org/10.1093/nar/gku323 |
|
Genotype, Polymorphism, NGS/HTS |
| TEMP2 |
https://doi.org/10.1093/nar/gkab010 |
|
Genotype, Polymorphism, NGS/HTS, Short-Read |
| TE-nester |
https://ieeexplore.ieee.org/document/8621071 |
|
Structure, Nested Insertion |
| 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 |
| TEPEAK |
https://doi.org/10.1101/2023.10.13.562297 |
|
Genotype, Polymorphism, NGS/HTS |
| TEpeaks |
|
|
ChIP-Seq |
| tephra |
|
|
Homology, Library Generation, Structure, Classification, Age, Annotation |
| TEPID |
https://doi.org/10.7554/eLife.20777.001 |
|
Polymorphism, Genotype, NGS/HTS |
| TE-reX |
https://doi.org/10.1101/2020.07.02.163816 |
|
Genotype, Polymorphism, Recombination |
| TERAD |
https://doi.org/10.1111/1755-0998.13080 |
|
RAD-Seq, Repeat Masking, Annotation |
| TERL |
https://doi.org/10.1093/bib/bbaa185 |
|
Classification, Neural Network |
| TESD |
https://doi.org/10.1093/bioinformatics/btl454 |
|
Simulation, Genome |
| TESeeker |
https://doi.org/10.1186/1471-2105-12-130 |
|
Homology, VirtualBox, Library Generation |
| TEsmall |
https://doi.org/10.3389/fgene.2018.00461 |
|
NGS/HTS, Small RNA, piRNA, Annotation |
| TEsorter |
https://doi.org/10.1093/hr/uhac017 |
Link |
Classification, HMM |
| TEspeX |
https://doi.org/10.1093/bioinformatics/btac526 |
Zenodo |
NGS/HTS, Abundance, Expression, Transcription |
| TE-Tracker |
https://doi.org/10.1186/s12859-014-0377-z |
|
Polymorphism, Genotype |
| TETyper |
https://doi.org/10.1099/mgen.0.000232 |
|
Short-Read, Paired-End, Polymorphism, Genotype, Archaea, Bacteria |
| TeXP |
https://doi.org/10.1371/journal.pcbi.1007293 |
|
Expression, Transcription, RNA-Seq, NGS/HTS, LINE/Non-LTR Retrotransposon, Activity, Short-Read |
| The RIPper |
https://doi.org/10.7717/peerj.7447 |
Link |
RIP/Repeat-Induced Point Mutation, Mutation, GC, Repeat, Web Server |
| TIDAL |
https://doi.org/10.1093/nar/gkv1193 |
|
Genotype, Polymorphism, Illumina, Drosophila |
| TIDDIT |
https://f1000research.com/articles/6-664/v2 |
|
Rearrangement, NGS/HTS, Structural Variation |
| TideHunter |
https://doi.org/10.1093/bioinformatics/btz376 |
|
Long-Read, Tandem Repeat, NGS/HTS |
| TIDK (Telomere Identifcation toolKit) |
|
Github |
De Novo, Telomere, Visualization |
| TIGER (Target Integrative Genetic Element Retriever) |
https://doi.org/10.1093/nar/gkaa156 |
|
ICE/Integrative and Conjugative Element, Prophage/Bacteriophage |
| Tinscan |
|
|
Comparative, Polymorphism, Genotype |
| TinT (Transposition in Transposition) |
https://doi.org/10.1186/1471-2148-10-376 |
|
Nested Insertion, Web Server |
| TIF (Transposon Insertion Finder) |
https://doi.org/10.1186/1471-2105-15-71 |
|
NGS/HTS, Genotype, Polymorphism, Short-Read |
| TIP_finder |
https://doi.org/10.3390/biology9090281 |
|
NGS/HTS, Genotype, Polymorphism |
| TIPseq-Hunter |
https://doi.org/10.1073/pnas.1619797114 |
|
Paired-End, Illumina, Machine Learning |
| TIR-Finder |
https://doi.org/10.4137/EBO.S10619 |
|
ITR/TIR/DNA Transposon, Web Server, Homology, Structure |
| TIR-Learner |
https://doi.org/10.1016/j.molp.2019.02.008 |
|
ITR/TIR/DNA Transposon, Homology, Structure, Annotation |
| TIRMITE |
|
|
MITE, HMM, ITR/TIR/DNA Transposon, Annotation |
| T-lex |
https://doi.org/10.1093/nar/gkq1291 |
|
Genotype, Polymorphism, NGS/HTS |
| T-lex2 |
https://doi.org/10.1093/nar/gku1250 |
|
Genotype, Polymorphism, NGS/HTS |
| T-lex3 |
https://doi.org/10.1093/bioinformatics/btz727 |
|
Genotype, Polymorphism, NGS/HTS |
| TLDR |
https://doi.org/10.1101/2020.05.24.113068 |
|
NGS/HTS, Long-Read, Genotype, Polymorphism |
| TnComp_finder |
|
|
Composite Transposon |
| Tn3_finder |
https://doi.org/10.1128/mBio.00452-20 |
|
Transposon |
| Tn3+TA_finder |
https://doi.org/10.1128/mBio.00452-20 |
|
Transposon, Toxin-Antitoxin Loci |
| Tn-Core |
https://doi.org/10.1021/acssynbio.8b00432 |
|
Tn-Seq, Transposon Mutagenesis, RNA-Seq, Metabolic Modelling |
| TnPred |
http://dx.doi.org/10.1155/2012/678761 |
|
Web Server, Transposase, Archaea, Bacteria, IS Element |
| Tn-seq Explorer |
https://doi.org/10.1371/journal.pone.0126070 |
|
Tn-Seq, Transposon Mutagenesis |
| TRACKPOSON |
https://doi.org/10.1038/s41467-018-07974-5 |
|
Genotype, Polymorphism, Paired-End, NGS/HTS |
| TraDIS toolkit |
https://doi.org/10.1093/bioinformatics/btw022 |
|
Tn-Seq, Transposon Mutagenesis |
| TraFIC |
https://doi.org/10.1126/science.1251343 |
|
NGS/HTS, Paired-End, Homo sapiens, Genotype, Polymorphism |
| TRANScendence |
https://doi.org/10.1186/s12859-017-1824-4 |
|
De Novo, Homology, Structure, Library Generation, Annotation, Web Server |
| TRANSIT |
https://doi.org/10.1371/journal.pcbi.1004401 |
|
Tn-Seq, Transposon Mutagenesis |
| TRANSPO |
|
|
ITR/TIR/DNA Transposon, Homology |
| TranspoScope |
https://doi.org/10.1093/bioinformatics/btaa244 |
|
Genotype, Polymorphism, Visualization, NGS/HTS |
| Transposeq |
https://doi.org/10.1101/gr.163659.113 |
|
Polymorphism, Genotype, Web Server, Homo sapiens, Eukaryotic Retrotransposon |
| Transposome |
https://doi.org/10.1093/bioinformatics/btv059 |
|
De Novo, Assembly, Homology |
| Transposon Cluster Finder |
https://doi.org/10.1371/journal.pcbi.0030137 |
|
Nested Insertion |
| TransposonPSI |
|
|
BLAST, Eukaryotic Transposon |
| TransposonUltimate |
https://doi.org/10.1093/nar/gkac136 |
Link |
Eukaryotic Transposon, Library Generation, Classification, Annotation, Structural Variation |
| TranSurVeyor |
https://doi.org/10.1093/nar/gky685 |
|
Genotype, Polymorphism, Paired-End, NGS/HTS |
| 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 |
| T-REKS |
https://doi.org/10.1093/bioinformatics/btp482 |
|
Tandem Repeat |
| TRcaller |
https://doi.org/10.1101/2023.02.15.528687 |
|
Tandem Repeat, NGS/HTS, Long-Read, Short-Read |
| TrEMOLO |
https://doi.org/10.1101/2022.07.21.500944 |
|
NGS/HTS, Long-Read, Oxford Nanopore, Genotype, Polymorphism |
| TRF |
https://doi.org/10.1093/nar/27.2.573 |
|
Tandem Repeat |
| TRGT (Tandem Repeat Genotyping Tool) |
https://doi.org/10.1101/2023.05.12.540470 |
|
Tandem Repeat, PacBio, Long-Read, NGS/HTS, Genotype |
| TRiCoLOR |
https://doi.org/10.1093/gigascience/giaa101 |
|
Tandem Repeat, NGS/HTS, Long-Read |
| tRNAscan-SE- On-line |
https://doi.org/10.1093/nar/gkw413 |
Link |
tRNA |
| tRNA-DL |
https://doi.org/10.1159/000493215 |
|
tRNA, Deep Neural Network |
| TROLL |
https://doi.org/10.1093/bioinformatics/18.4.634 |
|
Tandem Repeat |
| TRTools |
https://doi.org/10.1101/2020.03.17.996033 |
|
Tandem Repeat, Genotype |
| 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 |
| TypeTE |
https://doi.org/10.1093/nar/gkaa074 |
|
Genotype, Polymorphism |
| UCSC Repeat Browser |
https://doi.org/10.1101/429613 |
|
Repeat, Visualization, Annotation |
| ULTRA |
https://doi.org/10.1145/3233547.3233604 |
|
Tandem Repeat, HMM, Repeat Masking |
| V-ELMpiRNAPred |
https://doi.org/10.1142/S0219720016500463 |
|
piRNA, Neural Network |
| VariationHunter |
https://doi.org/10.1093/bioinformatics/btq216 |
|
NGS/HTS, Genotype, Polymorphism, Homo sapiens |
| VHICA |
https://doi.org/10.1093/molbev/msv341 |
|
Horizontal Transfer |
| VirSorter |
https://doi.org/10.7717/peerj.985 |
|
Prophage/Bacteriophage, Homology, HMM |
| VirusSeq |
https://doi.org/10.1093/bioinformatics/bts665 |
|
Virus, RNA-Seq, Homo sapiens |
| VirusTaxo |
https://doi.org/10.1101/2021.04.29.442004 |
|
Virus, K-mer, Classification, Web Server |
| VISMapper |
https://doi.org/10.1186/s12859-017-1837-z |
|
Virus, NGS/HTS, Web Server, Genotype, Polymorphism, Insertion Site, Visualization |
| VisualTE |
https://doi.org/10.1186/s12864-015-1351-5 |
|
Annotation, Visualization |
| VisualRepbase |
https://doi.org/10.1186/1471-2105-9-345 |
|
Annotation, Visualization |
| vHULK (Viral Host UnveiLing Kit) |
https://doi.org/10.1101/2020.12.06.413476 |
|
Prophage/Bacteriophage |
| Vmatch |
|
|
Repeat Annotation |
| VRprofile |
https://doi.org/10.1093/bib/bbw141 |
|
Virulence, AMR/Antibiotic Resistance |
| VRprofile2 |
https://doi.org/10.1093/nar/gkac321 |
|
Virulence, AMR/Antibiotic Resistance |
| WGSSAT |
https://doi.org/10.1093/jhered/esx075 |
|
Simple Sequence Repeat/Microsatellite, Repeat Annotation, Primer |
| WtP (What the Phage) |
https://doi.org/10.1101/2020.07.24.219899 |
|
Prophage/Bacteriophage, Annotation, Classification, Pipeline |
| WindowMasker |
https://doi.org/10.1093/bioinformatics/bti774 |
|
Repeat Masking, Annotation, De Novo |
| Winnowmap2 |
https://doi.org/10.1101/2020.11.01.363887 |
|
Long-Read, NGS/HTS, Repeat |
| xenoGI |
https://doi.org/10.1186/s12859-018-2038-0 |
|
Genomic Island, Synteny, Phylogeny |
| xTea |
https://doi.org/10.1038/s41467-021-24041-8 |
|
Eukaryotic Transposon, Polymorphism, Genotype, Long-Read, Short-Read, Pangenome |
| YASS |
https://doi.org/10.1093/nar/gki478 |
|
Dot Plot, Visualization, Alignment, Web Server |
| YORO |
https://doi.org/10.1371/journal.pone.0291925 |
|
Classification, LTR Retrotransposon, Convolutional Neural Network |
| Zisland Explorer |
https://doi.org/10.1093/bib/bbw019 |
|
Genomic Island, GC |