Phylogeny:RT LTR retroelements

AP clan AA aspartic peptidasesAP Bel/PaoAP CaulimoviridaeAP Caulimoviridae dom2AP LTR retroelementsAP RetroviridaeAP Ty1/CopiaAP Ty3/GypsyATF CaulimovirusBel1 SpumaretrovirusBel2 SpumaretrovirusCHR Ty1/CopiaCHR eukaryote protein domainsCHR retroelementCOAT CaulimoviridaeCOATPOL CaulimoviridaeENV Athila (Ty3/Gypsy)ENV Errantiviridae (Ty3/Gypsy)ENV RetroviridaeENV Sire (Ty1/Copia)GAG Bel/PaoGAG RetroviridaeGAG Ty1/CopiaGAG Ty3/GypsyGAGPOL Bel/PaoGAGPOL RetroviridaeGAGPOL Ty1/CopiaGAGPOL Ty3/GypsyGPYF LTR retroelementsINT Bel/PaoINT GIN/GINGERINT LTR retroelementsINT RetroviridaeINT Ty1/CopiaINT Ty3/GypsyMOV CaulimoviridaeNEF LentiviridaeORF2 BadnavirusORFB SoymovirusORFC SoymovirusORFX BetaretrovirusPOL Bel/PaoPOL CaulimoviridaePOL LTR retroelementsPOL RetroviridaePOL Ty1/CopiaPOL Ty3/GypsyREV LentivirusREX LentivirusRNaseH Bel/PaoRNaseH CaulimoviridaeRNaseH LTR retroelementsRNaseH RetroviridaeRNaseH Ty1/CopiaRNaseH Ty3/GypsyRT Bel/PaoRT CaulimoviridaeRT LTR retroelementsRT RetroviridaeRT Ty1/CopiaRT Ty3/GypsySORF BetaretrovirusTAT LentivirusTAV CaulimoviridaeTAX DeltaretrovirusVAP CaulimoviridaeVIF-Q LentivirusVPR-VPX LentivirusdUTPase retroelements

Method of phylogenenetic reconstruction

Phylogenetic reconstruction inferred based on the LTR retroelemets reverse transcriptase using Felsenstein´s protein sequence parsimony method based on (Eck and Dayhoff 1966) and (Fitch 1971) to generate a majority-rule consensus tree (Margush and McMorris 1981). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference.