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. 2019 May 30;10(6):419. doi: 10.3390/genes10060419

Table 1.

Summary of tools commonly used for transposable elements (TE) detection and analysis. Methods that have been compared on human datasets in [155] are highlighted in bold.

Name of the Method Purpose Link Reference
Popoolation_TE2 TE detection in pooled designs https://sourceforge.net/p/popoolation-te2/wiki/Home/ [156]
T-LEX2 Detection of polymorphic TEs from short reads http://petrov.stanford.edu/cgi-bin/Tlex.html [157]
STEAK Detection of polymorphic TEs from short reads https://github.com/applevir/STEAK [158]
TIDAL Detection of polymorphic TEs from short reads http://www.bio.brandeis.edu/laulab/Tidal_Fly/Tidal_Fly_Home.html [159]
MELT Detection of polymorphic TEs from short reads http://melt.igs.umaryland.edu/ [153]
LoRTE Detection of polymorphic TEs from PacBio sequencing http://www.egce.cnrs-gif.fr/?p=6422 [160]
ITIS Detection of polymorphic TEs from short reads https://github.com/Chuan-Jiang/ITIS [161]
TEMP Detection of polymorphic TEs from short reads https://github.com/JialiUMassWengLab/TEMP [162]
Mobster Detection of polymorphic TEs from short reads http://sourceforge.net/projects/mobster/ [163]
Tangram Detection of polymorphic TEs from short reads https://github.com/jiantao/Tangram [164]
RetroSeq Detection of polymorphic TEs from short reads https://github.com/tk2/RetroSeq [165]
RelocaTE2 Detection of polymorphic TEs from short reads https://github.com/JinfengChen/RelocaTE2 [166]
McClintock Combination of several methods into a single pipeline https://github.com/bergmanlab/mcclintock [167]
Invade Population genomics modeling (forward-in-time) incorporating coevolution with piRNA clusters https://sourceforge.net/p/te-tools/code/HEAD/tree/sim3p/ [104]
SLIM3 Population genomics modeling (forward-in-time) https://messerlab.org/slim/ [79]