. 2005 Jan 7;33(1):162–170. doi: 10.1093/nar/gki159

Table 1.

Average sum-of-pairs costs for sets of intersection sub-blocks of multiple alignments from five programs on the CFTR, SCL, MET and ST7 data sets

Program	CFTR				SCL				MET				ST7
	S50^a	S65	S67	S70	S33	S36	S37	S39	S223	S258	S283	S315	S260	S295	S320	S353
T-COFFEE^b	1.574	1.579	1.601	1.610	1.560	1.582	1.579	1.595	1.545	1.553	1.555	1.560	1.509	1.524	1.528	1.537
MAP2	1.595	1.597	1.619	1.627	1.583	1.605	1.602	1.618	1.565	1.574	1.574	1.579	1.531	1.546	1.550	1.559
MLAGAN	1.649	1.648	N/A	N/A	1.604	1.624	1.622	N/A	1.601	1.610	N/A	N/A	1.573	1.586	1.590	N/A
CHAOS/DIALIGN	1.698	1.702	1.722	N/A	1.665	1.687	N/A	N/A	1.686	1.693	1.696	N/A	1.631	1.645	N/A	N/A
MAVID	1.762	N/A	N/A	N/A	1.810	N/A	N/A	N/A	1.719	N/A	N/A	N/A	1.701	N/A	N/A	N/A

^aThe name S50 means that a set of 50 intersection sub-blocks was selected from every multiple alignment. The number 1.649 on row MLAGAN and column S50 is the average sum-of-pairs cost of 50 intersection sub-blocks of blocks of the MLAGAN alignment that have an intersection with blocks of the MAP2 alignment. The mark N/A on row MLAGAN and column S70 means that the MLAGAN alignment does not contain 70 blocks that have an intersection with blocks of the MAP2 alignment.

^bThe set of intersection sub-blocks for T-COFFEE was generated from the corresponding set of blocks for MAP2 by running T-COFFEE, once for each MAP2 block, on the regions of the MAP2 block.