The Pseudoviridae / Copia taxonomy and phylogenetic relationships. (A) The inconsistency in the classification of LTR-RTNs between the ICTV and TE-based systems. (B) Neighbor-Joining phylogenetic tree with 1,000 bootstrap replicates based on the sequence of the pol polyprotein between the fifth RT conserved domain and the RNase H gene. Sireviruses (red circles, or red triangles if they were retrieved from MASiVEdb) form a monophyletic group, which is supported with 100% confidence by the bootstrap analysis. Pseudoviruses (blue diamonds) and Hemiviruses (brown squares) do not resolve in strongly-supported separate branches. Tpv2 (green triangle) is a single Pseudoviridae species of unknown genera classification.