Within the GyDB classification schema, LTR retrotransposons and relatives are subdivided based upon well supported phylogenetic groups. More details (reference sequences, HMMs) concerning this can be found at the resource itself (Llorens et al. 2010).
The theoretical framework for the GyDB classification is found in Llorens et al. (2009).
| URL | http://gydb.org/index.php/Main_Page |
|---|---|
| DOI | https://doi.org/10.1093/nar/gkq1061 |
| Type | Classification Schema |
| Root | Branch | Genus/Cluster | Clade |
|---|---|---|---|
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Plants | CRM |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Plants | Del |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Plants | Galadriel |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Plants | Reina |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Plants | REM1 |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Plants | G-Rhodo |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Fungi and vertebrates | Pyggy |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Fungi and vertebrates | MGLR3 |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Fungi and vertebrates | Pyret |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Fungi and vertebrates | Maggy |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Fungi and vertebrates | MarY1 |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Fungi and vertebrates | TF1-2 |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Fungi and vertebrates | V-Clade |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Undefined | Tse3 |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Undefined | Ty3 |
| Ty3/Gypsy | Branch 1 (Chromoviridae) | Undefined | Skipper |
| Ty3/Gypsy | Branch 2 | Athila/Tat | Athila |
| Ty3/Gypsy | Branch 2 | Athila/Tat | Tat |
| Ty3/Gypsy | Branch 2 | Errantiviridae | 17.6 |
| Ty3/Gypsy | Branch 2 | Errantiviridae | Gypsy |
| Ty3/Gypsy | Branch 2 | Metaviridae | 412/mdg1 |
| Ty3/Gypsy | Branch 2 | Metaviridae | Micropia/mdg3 |
| Ty3/Gypsy | Branch 2 | Metaviridae | Gmr1 |
| Ty3/Gypsy | Branch 2 | Metaviridae | Osvaldo |
| Ty3/Gypsy | Branch 2 | Metaviridae | Cer2-3 |
| Ty3/Gypsy | Branch 2 | Metaviridae | Cer1 |
| Ty3/Gypsy | Branch 2 | Metaviridae | CsRN1 |
| Ty3/Gypsy | Branch 2 | Metaviridae | Tor1 |
| Ty3/Gypsy | Branch 2 | Metaviridae | Tor2 |
| Ty3/Gypsy | Branch 2 | Metaviridae | Tor4 |
| Ty3/Gypsy | Branch 2 | Metaviridae | Cigr-1 |
| Ty3/Gypsy | Branch 2 | Mag | A-Clade |
| Ty3/Gypsy | Branch 2 | Mag | B-Clade |
| Ty3/Gypsy | Branch 2 | Mag | C-Clade |
| Ty1/Copia | Branch 1 | Pseudovirus (Pseudoviridae) | Ty (Pseudovirus) |
| Ty1/Copia | Branch 1 | CoDi-I/CoDi-A | |
| Ty1/Copia | Branch 1 | CoDi-II/CoDi-B | |
| Ty1/Copia | Branch 1 | CoDi-C | |
| Ty1/Copia | Branch 1 | CoDi-D | |
| Ty1/Copia | Branch 1 | GalEA | |
| Ty1/Copia | Branch 2 | p-Cretro | |
| Ty1/Copia | Branch 2 | Sirevirus (Pseudoviridae) | Sire |
| Ty1/Copia | Branch 2 | Sirevirus (Pseudoviridae) | Oryco |
| Ty1/Copia | Branch 2 | Retrofit | |
| Ty1/Copia | Branch 2 | Tork | |
| Ty1/Copia | Branch 2 | Osser | |
| Ty1/Copia | Branch 2 | PyRE1G1 | |
| Ty1/Copia | Branch 2 | Hydra | |
| Ty1/Copia | Branch 2 | Hemivirus (Pseudoviridae) | Copia |
| Ty1/Copia | Branch 2 | 1731 | |
| Ty1/Copia | Branch 2 | Tricopia | |
| Ty1/Copia | Branch 2 | Mtanga | |
| Ty1/Copia | Branch 2 | Humnum | |
| Bel/Pao | Branch 1 | Semotivirus | Tas |
| Bel/Pao | Branch 1 | Semotivirus | Bel |
| Bel/Pao | Branch 2 | Semotivirus | Pao |
| Bel/Pao | Branch 2 | Semotivirus | Sinbad |
| Bel/Pao | Branch 3 | Semotivirus | Suzu |