prev_root_c2 = prev_root.getChildNode2();
prev_root_was_dup = prev_root.isDuplication();
final PhylogenyBranch current_branch = branches.get( j );
prev_root_c2 = prev_root.getChildNode2();
prev_root_was_dup = prev_root.isDuplication();
final PhylogenyBranch current_branch = branches.get( j );