Table 1:

ClustalW alignment optimisation using UIMA

MSA programme	Reference 1 Equidistant sequences		Reference 2 Family with orphans	Reference 3 Divergent subfamilies	Reference 4 Large extensions	Reference 5 Large insertions	Total running time (min)
	V1: <20%	V2: 20–40%
ClustalW version 1.83	0.46	0.85	0.86	0.62	0.75	0.61	98.6
Optimised ClustalW	0.50	0.87	0.86	0.65	0.77	0.63	40.4

Mean SP scores for each reference set in the BAliBASE multiple alignment benchmark