Phylogeny:AP Caulimoviridae

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 protease protein (AP) product encoded by the pol internal region of the Caulimoviridae family, and on a second non-pol protease-like domain encoded by the ORF7 of three soymoviruses and by the C-terminus of CSVMV-ORF I Cavemovirus (downstream to the MOV region) (highlighted in red). The tree has been realized using MEGA 4.1 (Kumar et al. 2008) and the Neighbor joining (NJ) method of phylogenetic reconstruction (Saitou and Nei 1987) with 100 bootstrap replicates under the conditions: uniform rates among sites and pairwise deletion of gaps.