AB-BLAST |
Most sensitive, fastest and flexible core BLAST engine, target
your searches easier and get better results faster
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BLASTER suite |
Developed for transposable element search and their annotation
in large eukaryotic genome sequence
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Censor |
Compares and masks protein or nucleotide sequences
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HERVd |
Simple and fast environment for screening human genome for
HERVs (=Human endogenous retroviruses)
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IS Finder |
Provides a list of insertion sequences isolated from
eubacteria and archae
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LTR_FINDER |
An efficient program for finding full-length LTR
retrotranspsons in genome sequences
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LTRdigest |
Automated annotation of internal features of LTR retrotransposons
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LTRharvest |
De novo detection of LTR retrotransposons
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LTR_STRUC |
Scans nucleotide sequence files for LTR retrotransposons
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MGEScan-LTR |
Long terminal repeat (LTR) retroelements discovery
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MGEScan-nonLTR |
Non-long terminal repeat (non-LTR) retrotransposons discovery
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microTranspoGene |
The influence of Transposed Elements (TEs) on the biogenesis
of microRNAs
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MITE-Hunter |
Discovering miniature inverted-repeat transposable elements
from genomic sequences
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PClouds |
The P-clouds package is designed to identify repeat structure in large eukaryotic genomes using oligonucleotide counts. |
PILER |
A software for analyzing repetitive DNA found in genome sequences |
REannotate |
Automated Molecular Paleontology of Complex DNA Repeats
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RECON |
A package for automated de novo identification of repeat families from genomic sequences
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RepSeek |
A two-steps method (seed detection followed
by their extensions) that detects approximate repeats
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RepeatFinder |
Fnding repetitive sequences complete and draft genomes
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RepeatMasker |
Screens DNA sequences for interspersed repeats and low complexity DNA sequences
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RepeatModeler |
A de-novo repeat family identification and modeling package |
RepeatRunner |
A CGL-based program that integrates RepeatMasker with BLASTX
to provide a comprehensive means of identifying repetitive
elements
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repeat-match |
Ultra-fast alignment of large-scale DNA and protein sequences
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REPET |
The REPET package integrates bioinformatics programs in order to tackle biological issues at the genomic scale |
RepMiner |
Takes a graph theory approach to the classification and
assembly of the repetitive fraction of genomic sequence data
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REPuter |
Provides state of the art software solutions to compute and
visualize repeats in whole genomes or chromosomes
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RetroMap |
An application designed to help characterize LTR retroelements
on a genome scale in a visually interactive manner
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SMaRTFinder |
A command line tool to search biosequences for structured motifs
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Spectral Repeat Finder |
Find repeats through an analysis of the power spectrum of a
given DNA sequence
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Tallymer |
A collection of flexible and memory-efficient programs for
k-mer counting and indexing of large sequence sets.
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TARGeT |
Tree Analysis of Related Genes and Transposons
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TEclass |
Classifies unknown transposable element (TE) consensus sequences using machine learning approach
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TE Displayer |
TE Displayer can be used to retrieve genetic polymorphisms caused by transposable elements (TEs) in large-genomic datasets and present the results on virtual gel images |
TESD |
Provides a complete application that allows modellers to
implement other models of TE dynamics
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TESeeker |
TESeeker implements an automated homology-based approach for identifying transposable elements
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TinT |
Considering the high frequency of transposed elements they
contribute significantly to genome evolution and encrypt
valuable information about the phylogenetic relationships of
their host species.
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TIPseqHunter |
Identifies insertion sites with high precision and reliability |
T-lex |
A computational pipeline to detect presence and/or absence of
annotated individual transposable elements (TEs) in sequenced
genomes using NGS data
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TRANSPO |
Searching for Transposons with known TIR
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TranspoGene |
The influence of Transposed Elements (TEs) on the transcriptome of seven metazoan species
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Transposon-PSI |
An analysis tool to identify protein or nucleic acid sequence
homology to proteins encoded by diverse families of
transposable elements
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TRAP |
Tandem Repeats Analysis Program
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TRF |
Tandem repeats finder: a program to analyze DNA sequences
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TROLL |
Tandem Repeat Occurrence Locator |
TSDfinder |
A PERL script to detect target site duplications |
Vmatch |
A versatile software tool for efficiently solving large scale
sequence matching tasks.
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