Missing branch rate (%)
Method	16S.M.aa_ag	16S.M	23S.M	23S.M.aa_ag	23S.E.aa_ag	23S.E	Avg error
SATé	5.08	5.70	10.12	10.90	6.59	6.67	7.51
ML(MAFFT)	4.16	5.70	11.90	10.90	7.69	6.67	7.84
ML(MAFFT-PartTree)	10.62	8.79	22.02	20.51	14.29	5.33	13.59
ML(Prank+GT)	7.62	11.40	14.29	19.23	27.47	6.67	14.45
ML(Muscle)	21.48	20.19	14.88	17.31	10.99	6.67	15.25
ML(ClustalW)	12.47	10.93	15.48	16.03	23.08	18.67	16.11
ML(ClustalW-quicktree) ‘	9.47	11.40	20.83	18.59	28.57	24.00	18.81
ML(Opal)	18.94	19.71	22.02	26.92	17.58	8.00	18.86
	Alignment SP-FN error (%)
Dataset	16S.M.aa_ag	16S.M	23S.M	23S.M.aa_ag	23S.E.aa_ag	23S.E	Avg error
SATé	22.72	21.98	29.29	28.42	22.15	21.16	24.3
MAFFT	22.59	21.79	28.61	28.26	19.46	18.48	23.2
MAFFT-PartTree	23.09	27.49	32.11	33.85	20.66	19.65	26.1
Prank+GT	40.73	42.40	44.93	44.06	37.32	35.52	40.8
Muscle	31.14	32.02	34.46	35.59	22.79	21.46	29.6
ClustalW	38.22	42.58	46.25	47.65	29.96	38.54	40.5
ClustalW-quicktree	37.49	40.96	48.38	43.84	26.57	28.07	37.6
Opal	27.71	32.36	32.22	35.01	26.64	21.61	29.3