Improving multiple sequence alignment by using better guide trees

BMC Bioinformatics

Table 2 Mean SP and TC scores on OXBench

		ClustalW		MSAProbs		Probalign		ProbCons		T-Coffee
		Adaptive	Original	Adaptive	Original	Adaptive	Original	Adaptive	Original	Adaptive	Original
SP	0%-100%	89.833	89.446	90.092	90.062	89.997	89.966	89.719	89.680	89.534	89.519
	0%-20%	48.219	42.944	45.140	44.840	44.308	43.576	45.390	44.140	44.883	43.818
	20%-40%	77.364	77.061	77.874	77.839	77.261	77.259	77.026	77.049	76.545	76.667
	40%-70%	93.982	93.778	94.569	94.542	94.691	94.688	94.220	94.233	94.146	94.139
	70%-100%	99.274	99.236	99.25	99.260	99.319	99.319	99.138	99.138	99.055	99.070
TC	0%-100%	80.409	80.189	81.696	81.703	81.642	81.680	80.895	80.880	80.680	80.513
	0%-20%	20.883	18.233	22.078	22.078	20.462	20.518	20.988	20.301	19.663	19.108
	20%-40%	57.570	57.255	59.863	59.817	59.107	59.379	58.277	58.340	57.968	57.938
	40%-70%	86.403	86.363	87.966	87.933	88.255	88.204	87.309	87.307	87.212	86.941
	70%-100%	98.005	97.913	97.972	98.093	98.135	98.135	97.616	97.616	97.442	97.402

Average SP score and average TC score of the alignments on OXBench generated by the five aligners with guide tree generated by adaptive method and by aligners' own. Rows show the average sum of pairs scores (SP) and total column scores (TC) multiplied by 100. The best results in each pair are shown in bold.

ISSN: 1471-2105