Transposable Elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis.
Following are the list of resource and location for TE discovery and TE detection:
BLASTER suite http://urgi.versailles.inra.fr/development/blaster/
Censor http://www.girinst.org/censor/download.php
find_ltr http://darwin.informatics.indiana.edu/cgi-bin/evolution/ltr.pl
FINDMITE http://jaketu.biochem.vt.edu/dl_software.htm
HMMER http://hmmer.janelia.org/
LTR_FINDER http://tlife.fudan.edu.cn/ltr_finder/
LTR_STRUC http://www.genetics.uga.edu/retrolab/data/LTR_Struc.html
LTR_MINER http://genomebiology.com/2004/5/10/R79/suppl/s7
LTR_par http://www.eecs.wsu.edu/~ananth/software.htm
MAK http://wesslercluster.plantbio.uga.edu/mak06.html
MaskerAid http://blast.wustl.edu/maskeraid/
mer-engine http://mer-engine.cshl.edu/mer-home.php
mreps http://bioinfo.lifl.fr/mreps/
PILER http://www.drive5.com/piler/
PLOTREP http://repeats.abc.hu/cgi-bin/plotrep.pl
RepBase http://www.girinst.org/
RepeatFinder http://cbcb.umd.edu/software/RepeatFinder/
RepeatGluer http://nbcr.sdsc.edu/euler/intro_tmp.htm
RepeatMasker http://www.repeatmasker.org/
RepeatRunner http://www.yandell-lab.org/repeat_runner/index.html
RepeatScout http://repeatscout.bioprojects.org/
repeat-match http://mummer.sourceforge.net/
REPuter http://www.genomes.de/
RetroMap http://www.burchsite.com/bioi/RetroMapHome.html
SMaRTFinder http://bioinf.dimi.uniud.it/software/software/smartfinder
Tandem Repeats Finder http://tandem.bu.edu/trf/trf.html
Transposon Cluster Finder http://www.mssm.edu/labs/warbup01/paper/files.html
TE nest http://www.plantgdb.org/prj/TE_nest/TE_nest.html
TRANSPO http://alggen.lsi.upc.es/recerca/search/transpo/transpo.html
TSDfinder http://www.ncbi.nlm.nih.gov/CBBresearch/Landsman/TSDfinder/
Tu Lab TE tools http://jaketu.biochem.vt.edu/dl_software.htm
WU-BLAST http://blast.wustl.edu
