Phylogeny of mollusc LINEs. Phylogenetic analyses performed on extracted RT-containing LINEs (see the Tree-based classification of ORF-containing LINE elements section). A Maximum likelihood SupFAM tree #2 obtained by constraining the monophyly of different LINE superfamilies as recovered by the Neighbor-Joining topology (see the Methods and Results sections). Numbers in parentheses next to the LINE superfamilies represent the number of annotated clusters and the total number of elements represented by the included clusters, respectively. All tested trees with relative bootstrap values can be found in Additional file 29 : Data S1. More detailed versions of the SupFAM tree #2 subtrees can be found in Additional files 13 , 14 , 15 , 16 , and 17 : Figs. S7, S8, S9, S10, and S11.
