Table 5.

P-values for each model condition and metric for the hypothesis test that P+BAli-Phy outperforms P(default) with respect to tree accuracy

	Delta-RF	Delta-RF
Data	RAxML	FastTree-2
Indelible M2	0.021	0.014
RNAsim	0.677	0.660
Rose L1	0.036	0.054
Rose M1	0.136	0.030
Rose S1	0.010	0.007

Values are based on one-sided Student’s T-test for differences between the two methods on each replicate. Bolded values indicate significant differences using a Benjamini-Hochberg procedure to control the false discovery rate at 5 % [33]