Repeat tools

Tool	DOI	Alternate URL	Keywords
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/10.1101/2020.12.10.419374		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, caulimovirid endogenous viral elements, plants
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/10.1101/2022.09.05.505575		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
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
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
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
Genome ARTIST	https://doi.org/10.1186/s13100-016-0061-0		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		github	Polymorphism, Structural Variation, Long-reads, 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
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
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
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
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
LongRepMarker	https://doi.org/10.1093/nar/gkab563		De Novo, K-mer, Library Generation, Long-Read, Short-Read
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
MEGAnE	https://doi.org/10.1101/2022.03.25.485726	Github	Genotype, Polymorphism, NGS/HTS, Short-Read
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
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
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
nf-repeatmasking	http://doi.org/10.5281/zenodo.1134750		Repeat Masking, Classification
ngs_te_mapper	https://doi.org/10.1371/journal.pone.0030008		Target Site Duplication, Homology, NGS/HTS
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
PAI-IDA	https://doi.org/10.1016/S0378-1097(03)00204-0		Genomic Island, GC, Codon Usage
PaliDIS	https://doi.org/10.1101/2022.06.27.497710		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
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
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/10.1101/2022.05.22.493013		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
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
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
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
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)			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
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
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
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/10.21203/rs.3.rs-1723759/v1		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
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		Genomics, TE density, Genomic distribution of TE
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
Tedna	https://doi.org/10.1093/bioinformatics/btu365		Assembly, Illumina, Paired-End, 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

¶ Description

¶ Overview of tools for repeat analysis