( ( I ( ( do n't ) ( think ( I ( 've ( abandoned ( ( using clades ) ( at all ) ) ) ) ) ) ) ) ( , ( it ( ( 's ( just ( that ( I ( 'm ( using ( ( gene clades ) ( instead ( of ( organism clades ) ) ) ) ) ) ) ) ) ) . ) ) ) )
(ROOT (S (S (NP (PRP I)) (VP (VBP do) (RB n't) (VP (VB think) (SBAR (S (NP (PRP I)) (VP (VBP 've) (VP (VBN abandoned) (S (VP (VBG using) (NP (NNS clades)) (ADVP (IN at) (DT all))))))))))) (, ,) (NP (PRP it)) (VP (VBZ 's) (SBAR (RB just) (IN that) (S (NP (PRP I)) (VP (VBP 'm) (VP (VBG using) (NP (NP (NN gene) (NNS clades)) (PP (RB instead) (IN of) (NP (NN organism) (NNS clades))))))))) (. .)))
I don't think I've abandoned using clades at all, it's just that I'm using gene clades instead of organism clades.
(ROOT (S (NP (DT A) (NN clade)) (VP (VBZ is) (NP (NP (CD one) (NN way)) (PP (IN of) (NP (VBG classifying) (NNS organisms))))) (. .)))