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Tandem repeat detection software tools | Genome annotation

Tandem repeats (TRs) represent one of the most prevalent features of genomic sequences. Due to their abundance and functional significance, a plethora of detection tools has been devised over the last two decades. Source text: Schaper et al., 2012.

GMATA
Desktop

GMATA Genome-wide Microsatellite Analyzing Tool Package

Provides new strategies and complete solutions for fast simple sequence repeats…

Provides new strategies and complete solutions for fast simple sequence repeats (SSR) analyses, marker development, polymorphism screening by mapping and graphical display of results in a genome…

TRF
Desktop
Web

TRF Tandem Repeats Finder

An algorithm for finding tandem repeats in DNA sequences without the need to…

An algorithm for finding tandem repeats in DNA sequences without the need to specify either the pattern or pattern size. TRF uses the method of k-tuple matching to avoid the need for full scale…

REPuter
Desktop
Web

REPuter

Detection of various types of repeats is provided together with an evaluation…

Detection of various types of repeats is provided together with an evaluation of significance and interactive visualization.

ExpansionHunter
Desktop

ExpansionHunter

Determines pathogenic repeat expansions from paired end, Polymerase Chain…

Determines pathogenic repeat expansions from paired end, Polymerase Chain Reaction (PCR)-free and whole-genome sequencing (WGS) data. ExpansionHunter computes the maximum-likelihood genotype…

SciRoKo
Desktop

SciRoKo SSR Classification and Investigation by Robert Kofler

A user-friendly software tool for the identification of microsatellites in…

A user-friendly software tool for the identification of microsatellites in genomic sequences. The combination of an extremely fast search algorithm with a built-in summary statistic tool makes…

T-REKS
Desktop
Web

T-REKS

A program for ab initio identification of the tandem repeats. T-REKS is based…

A program for ab initio identification of the tandem repeats. T-REKS is based on clustering of lengths between identical short strings by using a K-means algorithm. T-REKS being linked to the Protein…

Repseek
Desktop

Repseek

An implementation of a two-steps method (seed detection followed by their…

An implementation of a two-steps method (seed detection followed by their extension) that detects those approximate repeats.

RIPCAL
Desktop

RIPCAL

Detects and identifies repeat-induced point mutation (RIP) in fungal genome.…

Detects and identifies repeat-induced point mutation (RIP) in fungal genome. RIPCAL is a software developed with alignment-based method associated to RIP index. It allows users to parameter several…

Swelfe
Web

Swelfe

Finds internal repeats at three levels. Swelfe identifies repeats by alignment…

Finds internal repeats at three levels. Swelfe identifies repeats by alignment of DNA sequences, amino acids sequences and three dimensional (3D) structures. Preliminarily, 3D structures are encoded…

tantan
Desktop

tantan

Masks simple regions (low complexity and short-period tandem repeats) in DNA,…

Masks simple regions (low complexity and short-period tandem repeats) in DNA, RNA, and protein sequences. The aim of tantan is to prevent false predictions when searching for homologous regions…

mreps
Desktop
Web

mreps

Allows identification of tandemly repeated structures in DNA sequences. mreps…

Allows identification of tandemly repeated structures in DNA sequences. mreps is constituted by an exhaustive combinatorial algorithms used to find all repeats verifying certain mathematical…

G T A T C G C T A
GECKO-CSB
Desktop

GECKO-CSB GEnome Comparison with K-mers Out-of-core-Computational Synteny Block

A package which detects and identifies blocks of large rearrangements taking…

A package which detects and identifies blocks of large rearrangements taking into account repeats, tandem repeats and duplications, starting with the simple collection of ungapped local alignments.…

SA-SSR
Desktop

SA-SSR

An innovative algorithm based on suffix and longest common prefix arrays for…

An innovative algorithm based on suffix and longest common prefix arrays for efficiently detecting simple sequence repeats (SSRs) in large sets of sequences. Existing SSR detection applications are…

findIR
Desktop

findIR

Detects perfect inverted repeats (IRs) from genome-scale inputs. findIR…

Detects perfect inverted repeats (IRs) from genome-scale inputs. findIR localizes the boarder positions of perfect IRs using a cumulative scoring system. It is based on assigning prime number scores…

ProGeRF
Web
Desktop

ProGeRF Proteome and Genome Repeat Finder Utilizing a Fast Parallel Hash Function

Extracts repetitive regions from genome and proteome sequences. ProGeRF was…

Extracts repetitive regions from genome and proteome sequences. ProGeRF was designed to be efficient, fast, and accurate and primarily user-friendly web tool allowing many ways to view and analyse…

IGRhCellID
Dataset

IGRhCellID Integrated Genomic Resources of Human Cell Lines for Identification

Collects genomic resources of common human cell lines. IGRhCellID provides…

Collects genomic resources of common human cell lines. IGRhCellID provides short tandem repeat (STR) profiles of human cell lines and tools with conventional laboratory polymerase chain reaction…

RepeatAnalyzer
Desktop

RepeatAnalyzer

A software tool for storing, managing, identifying and analysing short-sequence…

A software tool for storing, managing, identifying and analysing short-sequence repeats for the purpose of strain identification. RepeatAnalyzer can take a gene sequence and return the repeats it…

PerPlot
Web

PerPlot Periodicity Plot

Detects predominant periodicities in a nucleotide sequence. PerPlot counts the…

Detects predominant periodicities in a nucleotide sequence. PerPlot counts the number of times a pair of A-tracts occur in the analyzed sequence at a mutual distance. The program reads a nucleotide…

RepLong
Desktop

RepLong

Allows users to determine de novo repeat elements. RepLong is a standalone…

Allows users to determine de novo repeat elements. RepLong is a standalone software which can be used for analyzing lower coverage data or complement existing methods to improve the repeat…

Kmer-SSR
Desktop

Kmer-SSR

Provides an exhaustive or filtered approach to finding all simple sequence…

Provides an exhaustive or filtered approach to finding all simple sequence repeats (SSRs) in a given sequence. Kmer-SSR is a method that utilizes k-mer decomposition. It provides SSR filters that are…

Lirex
Desktop

Lirex Long Inverted Repeats Explorer

Allows identification of long inverted repeats (LIRs) in a long genomic…

Allows identification of long inverted repeats (LIRs) in a long genomic distance. Lirex is a cross-platform tool which allows users to specify LIR searching criteria, such as length of the region, as…

TAREAN
Desktop

TAREAN TAndem REpeat Analyzer

Detects satellite repeats directly from unassembled short reads. TAREAN employs…

Detects satellite repeats directly from unassembled short reads. TAREAN employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. It takes paired-end…

MCScanX-transpo…
Desktop

MCScanX-transposed

Detects transposed gene duplications that occurred within different epochs.…

Detects transposed gene duplications that occurred within different epochs. MCScanX-transposed is also useful for integrative analysis of gene duplication modes. It can be used to study gene…

TRAP
Desktop

TRAP Tandem Repeats Analysis Program

A Perl program that provides a unified set of analyses for the selection,…

A Perl program that provides a unified set of analyses for the selection, classification, quantification and automated annotation of tandemly repeated sequences. TRAP uses the results of the Tandem…

STAR
Web
Desktop

STAR

Searches for significant approximate tandem repeats (ATR) of a given motif in a…

Searches for significant approximate tandem repeats (ATR) of a given motif in a DNA sequence. For each region of the sequence that is similar to a tandem repeat of the input motif, STAR returns a…

TRAL
Desktop

TRAL Tandem Repeat Annotation Library

Makes annotation of tandem repeats in amino acid and nucleic data simple. TRAL…

Makes annotation of tandem repeats in amino acid and nucleic data simple. TRAL includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs; statistical…

Red
Desktop

Red

A repeat-detection tool capable of labeling its training data and training…

A repeat-detection tool capable of labeling its training data and training itself automatically on an entire genome. Red is easy to install and use. It is sensitive to both transposons and simple…

IRF
Desktop

IRF Inverted Repeats Finder

A prototype tool for identifying approximate inverted repeats in nucleotide…

A prototype tool for identifying approximate inverted repeats in nucleotide sequences that is similar in concept to the Tandem Repeats Finder. Candidate IRs are detected by finding short, exact,…

MsDetector
Desktop

MsDetector

A software tool for DNA microsatellites (MSs) detection. The system is based on…

A software tool for DNA microsatellites (MSs) detection. The system is based on a hidden Markov model and a general linear model. The user is not obligated to optimize the parameters of MsDetector.…

Palindrome…
Web

Palindrome Analyser

Allows visualization and analysis of inverted repeats in various nucleotide…

Allows visualization and analysis of inverted repeats in various nucleotide sequences including circular genomes. Palindrome Analyser compares the frequency and types of inverted repeats across…

SBARS
Desktop

SBARS Spectral-Based Approach for Repeats Search

A fast and efficient tool for identifying dispersed (direct, inverted) and…

A fast and efficient tool for identifying dispersed (direct, inverted) and tandem DNA repeats. The program is not aimed at the comparison of individual nucleotides. The main idea of this approach is…

LEPSCAN
Web

LEPSCAN LatEnt Periodicity SCANner

A web server for searching latent periodicity based on the method of modified…

A web server for searching latent periodicity based on the method of modified profile analysis (MPA). LEPSCAN allows searching latent periodicity in presence of insertions and deletions. Period…

QDD
Web
Desktop

QDD

An open access program providing a user-friendly tool for microsatellite…

An open access program providing a user-friendly tool for microsatellite detection and primer design from large sets of DNA sequences.

detectIR
Desktop

detectIR

A MATLAB-based program for the perfect and imperfect inverted repeat detection…

A MATLAB-based program for the perfect and imperfect inverted repeat detection that utilizes complex numbers and vector calculation and allows genome-scale data inputs. detectIR uses an algorithm to…

RepMaestro
Desktop

RepMaestro

Offers scalable and memory-conscious algorithms for finding supermaximal…

Offers scalable and memory-conscious algorithms for finding supermaximal repeats, maximal unique matches (MuMs) and tandem repeats in large genome sequences on disk. RepMaestro, similar to the…

TROLL
Desktop

TROLL Tandem Repeat Occurrence Locator

A light-weight simple sequence repeat (SSR) finder based on a slight…

A light-weight simple sequence repeat (SSR) finder based on a slight modification of the Aho-Corasick algorithm. TROLL is designed to have a powerful yet simple interface. The operation is performed…

STRING
Desktop

STRING Search for Tandem Repeats IN Genomes

Finds all significant tandem repeats. STRING is powerful, since it has…

Finds all significant tandem repeats. STRING is powerful, since it has successfully coped also with the longest segments of sequences in databases (up to millions of bases). It is portable,…

WM
Desktop

WM WindowMasker

Identifies and masks highly repetitive DNA sequences in a genome, using only…

Identifies and masks highly repetitive DNA sequences in a genome, using only the sequence of the genome itself. WM is orders of magnitude faster than RM because WM uses a few linear-time scans of the…

MREPATT
Web

MREPATT Multiple consecutive REpeated PATTerns in DNA sequences

A program to determine the number, length and position of exact consecutive…

A program to determine the number, length and position of exact consecutive repeats of short sequences in DNA fragments or whole genomes. The program also gives the statistical significance of…

OMWSA
Desktop

OMWSA Optimized Moving Window Spectral Analysis

A method and a visualization tool for DNA repeat detection. The spectrogram…

A method and a visualization tool for DNA repeat detection. The spectrogram obtained by OMWSA can clearly display the general distribution of repetitive sequences. More importantly, the repeats…

BASARD
Desktop

BASARD Bayesian Approach for Short Adjacent Repeat Detection

A Bayesian approach to detect short adjacent repeats in a de novo fashion. To…

A Bayesian approach to detect short adjacent repeats in a de novo fashion. To improve computing efficiency, we use a collapsing technique to reduce the dimension of the parameter space. After the…

SRF
Web

SRF Spectral Repeat Finder

Finds repeats through an analysis of the power spectrum of a given DNA…

Finds repeats through an analysis of the power spectrum of a given DNA sequence. By repeat we mean the repeated occurrence of a segment of N nucleotides within a DNA sequence. The repeats can be…

TRStalker
Web

TRStalker

An efficient heuristic algorithm for finding Fuzzy tandem repeats (TRs) in…

An efficient heuristic algorithm for finding Fuzzy tandem repeats (TRs) in biological sequences. TRStalker aims at improving the capability of TR detection for a class of fuzzy TRs for which existing…

PRAP
Desktop

PRAP Prokaryotic Repeats Annotation Program

Automates the analysis of repeats in both finished and draft genomes. It is…

Automates the analysis of repeats in both finished and draft genomes. It is aimed at identifying full spectrum repeats at the scale of the prokaryotic genome. Compared with the major existing repeat…

PILER
Desktop

PILER

An approach to de novo repeat annotation that exploits characteristic patterns…

An approach to de novo repeat annotation that exploits characteristic patterns of local alignments induced by certain classes of repeats. PILER is a package of efficient search algorithms for…

SATFIND
Web

SATFIND

Determines the position of long tandem repeats (satellites). SATFIND finds the…

Determines the position of long tandem repeats (satellites). SATFIND finds the localization of clusters of any short sequence (<12 bases) repeated a minimum number of times in regions with a fixed…

XSTREAM
Desktop
Web

XSTREAM

A powerful genome data-mining tool designed to efficiently identify tandem…

A powerful genome data-mining tool designed to efficiently identify tandem repeat (TR) patterns in biological sequence data. XSTREAM uses a seed-extension strategy coupled with several…

PrimerPipeline
Desktop

PrimerPipeline

Serves for microsatellite mining. PrimerPipeline is a program also dedicated to…

Serves for microsatellite mining. PrimerPipeline is a program also dedicated to primer design for de novo low coverage genomes. It allows users to search microsatellites and to design primers. It can…

Vmatch
Desktop

Vmatch

Solves efficiently large scale sequence matching tasks. Vmatch is a versatile…

Solves efficiently large scale sequence matching tasks. Vmatch is a versatile software that can process sequences over any user defined alphabet not larger than 250 symbols. This method fully…

einverted
Desktop

einverted

Finds inverted repeats (stem loops) in nucleotide sequences. einverted…

Finds inverted repeats (stem loops) in nucleotide sequences. einverted identifies regions of local alignment of the input sequence and its reverse complement that exceed a threshold score. The…

etandem
Desktop

etandem

Finds tandem repeats in a nucleotide sequence. etandem calculates a consensus…

Finds tandem repeats in a nucleotide sequence. etandem calculates a consensus sequence for a putative repeat region and scores potential repeats based on the number of matches and mismatches there…

equicktandem
Desktop

equicktandem

Finds tandem repeats in nucleotide sequences. equicktandem identifies regions…

Finds tandem repeats in nucleotide sequences. equicktandem identifies regions in a nucleotide sequence which are likely to contain tandem repeats. It must be no larger than a specified maximum repeat…

palindrome
Desktop

palindrome

Finds inverted repeats (stem loops) in nucleotide sequences. palindrome is an…

Finds inverted repeats (stem loops) in nucleotide sequences. palindrome is an Emboss tool that will find inverted repeats that include a proportion of mismatches and gaps, that correspond to bulges…

FAIR
Web

FAIR Find All Internal Repeats

A web server which has been deployed to identify the internal sequence repeats…

A web server which has been deployed to identify the internal sequence repeats in protein as well as DNA sequences. FAIR has been tested with a protein sequence of more than 35000 residues available…

ACMES
Web

ACMES Advanced Content Matching Engine for Sequences

A web server for the life sciences community to use to search for short repeats…

A web server for the life sciences community to use to search for short repeats of DNA sequence of length between 3 and 10,000 bases within multiple species. This search employs a unique and fast…

Trepeats
Desktop

Trepeats

An efficient algorithm for finding all tandem repeats within a sequence, under…

An efficient algorithm for finding all tandem repeats within a sequence, under the edit distance measure. Trepeats automates the task of listing all repeats that occur in a biological sequence. The…

SAT
Web
Desktop

SAT SSR Analysis Tool

Facilitates the integration, analysis and display of sequence data from simple…

Facilitates the integration, analysis and display of sequence data from simple sequence repeats (SSR) enriched libraries. SAT was designed to successively perform base calling and quality evaluation…

BWtrs
Web

BWtrs Burrows-Wheeler Tandem Repeat Searcher

A very efficient, web-based tool for large scale searching for exact tandem…

A very efficient, web-based tool for large scale searching for exact tandem repeats in genomes, based on the use of the Burrows-Wheeler transform. BWtrs is a remarkably efficient and powerful…

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