Table 1

Missing branch rates and alignment SP-FN error rates. For each statistic and model, the best-performing methods (within 1%) are in boldface. The best overall is indicated with an asterisk (*). For each “All models” entry, n = 600; for each easy entry, n = 120; for each moderate-to-difficult entry, n = 180.

Moderate to difficultEasy
All models10005001000500
Method% (SE)% (SE)% (SE)% (SE)% (SE)
Missing branch rate
RAxML(TrueAln)7.4 (0.1)9.3 (0.1)8.4 (0.1)5.1 (0.1)5.3 (0.1)
SATé*9.1 (0.2)*13.1 (0.3)*10.4 (0.2)*5.1 (0.1)5.4 (0.1)
RAxML(Prank+GT)13.0 (0.3)21.0 (0.6)15.2 (0.4)*5.1 (0.1)*5.3 (0.1)
RAxML(MAFFT)12.6 (0.4)21.6 (0.6)13.5 (0.3)*5.1 (0.1)*5.3 (0.1)
RAxML(Muscle)15.3 (0.5)22.9 (1.0)20.5 (0.9)5.4 (0.1)5.8 (0.1)
RAxML(ClustalW)21.6 (0.6)38.7 (0.7)21.6 (0.6)5.3 (0.1)5.7 (0.1)
Alignment SP-FN error rate
SATé*14.2 (0.6)*25.0 (1.3)*21.3 (0.7)*0.4 (0.02)*1.0 (0.1)
Prank+GT18.5 (0.8)30.6 (1.2)29.9 (1.1)*0.4 (0.02)1.1 (0.1)
MAFFT20.6 (0.8)38.6 (1.3)28.5 (1.0)0.9 (0.1)1.7 (0.1)
Muscle22.7 (0.9)34.0 (1.4)38.5 (1.5)1.8 (0.1)2.9 (0.2)
ClustalW46.9 (1.3)77.1 (1.1)64.1 (1.2)9.8 (0.5)12.9 (0.6)