Table 1.

Topological Accuracy of Tree-Building Methods on Simulated Protein Alignments with Gaps

	Topological Accuracy
Method	Distances	n = 10	n = 50	n = 250	n = 1,250	n = 5,000
PhyML	JTT	0.744a	0.771a	0.817a	0.801a	—
FastTree	Log-corrected	0.724b	0.763b	0.797b	0.778b	0.763b
FastME	Log-corrected	0.716c	0.754c	0.796b	0.777b	0.753c
BIONJ	Log-corrected	0.725b	0.754c	0.766c	0.730c	0.723c
BIONJ	JTT	0.701c	0.758c	0.777c	0.737c	0.731c
BIONJ	JTT + Γ	0.567c	0.625c	0.737c	0.697c	—
QuickTree	Log-corrected	0.716c	0.746c	0.760c	0.726c	0.716c
QuickTree	%Different	0.673c	0.678c	0.699c	0.672c	0.655c
Clearcut	Log-corrected	0.682c	0.733c	0.755c	0.723c	0.715c

^aSignificantly more accurate than FastTree (P < 0.01, paired t-test)

^bNot significantly different from FastTree (P > 0.01, paired t-test)

^cSignificantly less accurate than FastTree (P < 0.01, paired t-test)