Phylogeny:AP LTR retroelements
Method of phylogenenetic reconstruction
Phylogenetic reconstruction inferred based on the protease protein (AP) -encoded by the pol internal region common to Ty3/Gypsy, Retroviridae, Bel/Pao, Caulimoviridae and Ty1/Copia LTR retroelement families- 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 reconstructed 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