Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost

Table 1 List of evaluated programs

program	version	option
PRIME_piecewise		blosum62, g(x) = max{-(x + 9), -(0.5x + 21.5)}
PRIME_affine		blosum62, g(x) = -(x + 9)
Prrn [9]	3.4	-b2 -mblosum62 -u1 -v9
MAFFT* [15]	5.662	--maxiterate 1000 --localpair (L-INS-i)
ProbCons* [16]	1.09	default
T-Coffee* [27]	2.02	default
MUSCLE [8]	3.52	default
DIALIGN-T [28]	0.2.1	default
POA [5]	2	-do_global -do_progressive blosum80_trunc.mat
ClustalW [7]	1.83	default

Programs with * employ pairwise alignment information when calculating multiple alignment. Parameters or options of each program other than the gap penalty ones are chosen to obtain as accurate an alignment as possible.

ISSN: 1471-2105