( ( ( ( ( Often ( prokaryotes ( ( are all ) ( called bacteria ) ) ) ) , ) however ) ( ( some prokaryotes ) ( ( are not ) ( bacteria ( but archaea ) ) ) ) ) . )
(ROOT (S (S (ADVP (RB Often)) (NP (NNS prokaryotes)) (VP (VBP are) (RB all) (VP (VBN called) (NP (NNS bacteria))))) (, ,) (ADVP (RB however)) (S (NP (DT some) (NNS prokaryotes)) (VP (VBP are) (RB not) (NP (NP (NNS bacteria)) (PP (CC but) (NP (NN archaea)))))) (. .)))
Often prokaryotes are all called bacteria, however some prokaryotes are not bacteria but archaea.
(ROOT (S (NP (NNS Bacteria) (CC and) (NNS archaea)) (VP (VBP are) (NP (NP (NNS examples)) (PP (IN of) (NP (NNS prokaryotes))))) (. .)))