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] |