Optimized parameters.
Tabstop=4.

T99 templates
Algorithm	score	gapopen		gapextend	center

YL			0.863	0.22 		0.024 		0.42  
YLF			0.838	0.40 		0.04 		0.42 	
YLD			0.848	0.425 		0.0465 		0.795  
YLDF		0.830	0.90 		0.14 		0.34  
MM			0.857	3.60 		0.25 		4.265  
MdotF		0.860	3.00 		0.30 		-0.16 	
MdotP		0.856	1.60 		0.49 		-0.47 	
MdotM		0.848	50.0 		17.0 		12.00 	
FdotF		0.844	0.30 		0.015 		0.013  
PdotP		0.850	0.15 		0.022 		0.067 	
FdotP		0.836	0.26 		0.022 		0.055  
AL			0.830	3.80 		0.30 		-0.48  
ALI			0.831	3.30 		0.16 		-0.58  
LA			0.835	1.40 		0.20 		-0.47  
LAI			0.839	2.04 		0.19 		-0.566  
RE			0.846	5.45 		0.45 		-2.11  
euclidf		0.808	0.50 		0.03 		-0.70  
euclidp		0.824	0.70 		0.07 		-0.39  
correlf		0.859	1.90 		0.20 		0.11  
correlp		0.859	1.60 		0.12 		0.21  
rankp		0.857	1.21 		0.09 		0.45  
rankf		0.856	1.10 		0.16 		0.17  
ref			0.784	4.00 		0.14 		-2.35  

---------------------------------------------------------------

PSI-BLAST templates
Algorithm	score	gapopen		gapextend	center

YL			0.839	0.16 		0.024 		0.439  
YLF			0.820	0.49 		0.21 		0.41 	
YLD			0.832	0.42 		0.016 		0.798  
YLDF		0.830	0.90 		0.135 		0.38  
MM			0.837	3.20 		0.29 		4.43 	
MdotF		0.834	2.85 		0.28 		-0.115  
MdotP		0.838	2.135 		0.131 		-0.509  
MdotM		0.817	30.0 		11.0 		10.0  
FdotF		0.801	0.28 		0.01 		0.014  
PdotP		0.838	0.20 		0.012 		0.061  
FdotP		0.811	0.20 		0.034 		0.065  
AL			0.835	3.70 		0.15 		-0.56  
ALI			0.833	3.25 		0.12 		-0.53  
LA			0.802	1.44 		0.14 		-0.37  
LAI			0.805	2.52 		0.25 		-0.33  
RE			0.826	6.175 		0.585 		-2.115
ref			0.703	6.50 		0.03 		-2.00  
rankp		0.829	1.20 		0.08 		0.425  
rankf		0.842	0.65 		0.04 		0.24  
correlf		0.831	2.10 		0.07 		0.10  
correlp		0.840	1.72 		0.10 		0.22  
euclidf		0.804	0.70 		0.10 		-0.68  
euclidp		0.815	0.66 		0.022 		-0.356  

---------------------------------------------------------------

T99 prof-seq

AL			0.817	5.3 		0.355 		-0.68  
PdotP		0.818	0.147 		0.0065		0.0611

-end-