PnpProbs: a better multiple sequence alignment tool by better handling of guide trees

BMC Bioinformatics

Table 1 Average SP and TC scores on OXBench

	ALL (0–100 %)		0 %–20 %		20 %–50 %		50 %–100 %		Time
	SP	TC	SP	TC	SP	TC	SP	TC	mm:ss
PNPProbs	90.41	82.23	48.98	24.88	83.47 ^∗	68.79	98.05	95.18	2:58
GLProbs	90.38 ^∗	82.14 ^∗	47.29 ^∗	22.95 ^∗	83.48	68.65 ^∗	98.05	95.18	3:15
MSAProbs	90.07	81.75	44.83	22.08	82.77	67.74	98.01	95.08	4:04
Probalign	89.97	81.68	43.58	20.51	82.53	67.46	98.05	95.18	2:10
CONTRAlign	89.34	79.87	44.76	17.83	81.56	64.75	97.55	94.10	10:19
ProbCons	89.68	80.86	44.15	20.30	82.06	66.33	97.84	94.61	1:48
MUSCLE	89.50	80.67	45.64	21.90	81.75	66.15	97.63	94.28	0:19
MAFFT	88.00	77.96	37.82	13.27	78.99	60.86	97.41	93.68	0:19
T-Coffee	89.52	80.50	43.99	19.11	81.82	65.85	97.75	94.38	15:05
Clustal Ω	88.91	79.99	39.09	16.38	80.71	64.49	97.76	94.58	0:12
ClustalW	89.43	80.16	42.94	18.23	81.67	65.01	97.76	94.40	0:22
PicXAA	89.64	80.74	45.11	22.04	81.86	65.91	97.84	94.55	4:26
DIALIGN	83.97	72.41	26.03	8.07	72.67	52.57	95.21	89.54	3:17
Align-m	86.95	76.06	28.36	12.74	76.35	57.54	96.95	92.60	21:14

The table shows the average SP and average TC score (multiplied by 100). The best and second best results in each column are marked in bold and with *, respectively. The last column shows the running time using a single CPU thread. Note that we use default parameters for all tools

ISSN: 1471-2105