Phylogenetic relationship between the integrases of Ginger1 (for ' Gypsy INteGrasE Related 1'), Ginger2 and Gypsy LTR retrotransposons. The tree, based on the multiple alignments in the zinc finger domain and the DDE domain (see Additional file 1), is constructed by the minimum evolution (ME) method (Poisson correction model, pairwise deletion, gamma parameter = 2, bootstrap replicates = 1,000). The neighbor-joining (NJ) tree is shown in Additional file 2. The ME and NJ bootstrap values of major clades are shown in parenthesis, respectively. Lines in non-black colors differentiate the non-Gypsy integrases. The names of known Gypsy lineages follow previous literatures [18, 20, 43, 44]. The eukaryotic IS481-like integrases in Trichomonas vaginalis are designated as IS418EU. The two distinct Copia clades  are named Copia-I and Copia-II, respectively. Integrases containing the YPYY motif are marked with red dots. The clades containing the GPY/F motif are marked with green dots.