Table 1.

Reference-dependent alignment accuracy on the In-House benchmark

Methods	TMalign	Dali	Matt	DeepAlign
HHpred(Local)	32.63	36.60	35.53	35.47
HHpred(Global)	38.80	43.65	42.48	42.78
BThreader	37.44	41.85	40.17	40.95
CNFpred	46.49	51.77	49.98	51.19

Columns 2–5 indicate four different tools generating the reference alignments. Bold indicates the best performance.