Table 1.

Reference-dependent (Ref-dep) and reference-independent (Ref-ind) alignment accuracy on two benchmarks Set6K and Set4K

	Set6K		Set4K
	Ref-dep (%)	Ref-indTM	Ref-dep (%)	Ref-indTM
Our work	52	0.52	63	0.62
HHalign	45	0.44	57	0.56

Note: Reference-independent alignment accuracy is measured by TM-score.