Table 2.

The average TM-scores and GDT-TS scores of the 3D models generated from the 1,127 pairwise test alignments produced by HHsearch1.2, HHsuite and HMMsato

Method	Average TM-score	Average GDT- TS score
HHsearch (without secondary structure information)	0.527	0.459
HHsearch (with secondary structure information)	0.548	0.479
HHsuite (without secondary structure information)	0.525	0.459
HHsuite (with secondary structure information)	0.543	0.476
HMMsato	0.555	0.483

Bold numbers are the highest scores.